apraga/org - Change KNU6ADO757Q42ZLJUEVR6Z4FFSAWZKH6HZNSDNFMVONLEYBQIRIAC

Spip in T2T: done

Created by Alexis Praga on August 12, 2023

KNU6ADO757Q42ZLJUEVR6Z4FFSAWZKH6HZNSDNFMVONLEYBQIRIAC

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In channels

main

Change contents

Replacement in projects/bisonex.org at line 3 [4.35]

B:BD[3.16390] → [2.29:8221]

l#downloadAlt
- alt = séquences alternatives (utilisables)
- fix = patch (correction ou amélioration)
- random = séquence connue sur un chromosome mais non encore utilisée
** Pipelines prêt-à-l’emploi nextflow
Problème : nécessite singularity ou docker (ou conda)
Potentiellement utilisable avec nix...
** Validation : Quelles données de référence ?
Discussion avec Alexis
- Platinum genomes = génome seul
*** [[https://github.com/genome-in-a-bottle/giab_data_indexes][Genome in a bottle]]
  - NA12878 :
    - Illumina HiSeq Exome : fastq + capture en hg37
    - Illumina TruSeq Exome : bam, pas de capture
    - Exomes en hg37 https://zenodo.org/record/3597727 avec capture
      - HiSeq2000
      - NextSeq 500
      - HiSeq 2500
  - HG002,3,4
    - Illumina Whole Exome  : bam. le kit de capture est "Agilent SureSelect Human All Exon V5 kit" selon [[https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/OsloUniversityHospital_Exome_GATK_jointVC_11242015/README.txt][README]]. On il faut les régions [[https://kb.10xgenomics.com/hc/en-us/articles/115004150923-Where-can-I-find-the-Agilent-Target-BED-files-][selon ce site]]
      Un autre fichier est disponible (capture ???)
    https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/OsloUniversityHospital_Exome_GATK_jointVC_11242015/wex_Agilent_SureSelect_v05_b37.baits.slop50.merged.list
  "target region" +/- 50bp
    testé sur chr311780-312086 : ok
Autres technologies non adaptées au pipeline (vu avec Alexis)
*** [[https://www.illumina.com/platinumgenomes.html][Platinum genome
]] Que du génome « sequenced to 50x depth on a HiSeq 2000 system”
Genome possible
*** 1000 genomes
- intersection des capture + CCDS  [[id:b77e64fa-06a8-4ffa-8b5b-ab3fda684b61][Données brutes exome 1000 Genomes (fastq + capture)]]
- Broad instute : SureSelect human all exon v2 target capture kit : non disponible sur le site d'agilent (V6 ou plus)
*** Zone de capture
GIAB fourni le .bed pour l'exome . INfo : https://support.illumina.com/sequencing/sequencing_kits/nextera-rapid-capture-exome-kit/downloads.html
*** Valider la méthode
- 1000 genomes + SureSelect human all exon v2 target capture kit : non disponible sur le site d'agilent (V6 ou plus)
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2928-9
- GIAB + liftover du fichire de capture en hg38
Ce qui est aussi fait par
https://bcbio-nextgen.readthedocs.io/en/stable/contents/germline_variants.html
Mais avec UCSC liftover
** Centogène
https://www.twistbioscience.com/node/23906
Bed non fourni pour exactement cette capture
On prend https://www.twistbioscience.com/resources/data-files/twist-alliance-vcgs-exome-401mb-bed-files
qui content la majeure partie
* Réunion
** <2023-08-10 Thu> Alexis
Ok pour bloquer le développment d'ici mardi prochain
Dév:
- pipeline jusque VEP en T2T + GRCh38
- ok pour valider spip T2T sur quelques variant => à intégrer au pipeline
- annotation :
  - ok pour mobidetails hg38
  - +OMIM T2T+ non
  - +franklin hg38+ non pour le moment
- métriques (fastq a minima) + rapport multiqc
- optionnel
  - reformater la sortie
- on abandonne
  - XAMScissors ave indel
  - parallélisation haplotype caller
  - spliceai à la vollée
  - pangolin
Test
- GIAB:
  - hg38: ok pour refaire les tests NA12878 avec données cento, sinon ok pour "c'est difficile" sur les 3 fichiers de capture
  - T2T: ok pour faire des tests rapides mais probablement pas assez de temps !
- patient de synthèse : variant cento confirém par sanger seuls
Résultats
- ok pour scale up bwa mem et haplotyecaller
Manuscrit
- validation de méthode : laisser tomber la version actuelle et faire comme strasbourg (cf ngs diag) dans la présentatino
- a envoyé le powerponit avec les références des différsences articles
- ok pour robo4 si résultat
- architecture cible = VM : 78 coeurs 54Go RAUM et 1To espace disque
Passage en production : ok pour présentation rapide du code
* Nixpkgs :nix:
** DONE GATK
CLOSED: [2023-05-06 Sat 08:51]
*** DONE [[https://github.com/NixOS/nixpkgs/pull/185819][Binaire]]
CLOSED: [2022-09-10 Sat 23:53] SCHEDULED: <2022-08-10 Wed>
/Entered on/ [2022-08-09 Tue 10:57]
PR submitted
*** KILL Corriger code pour utiliser source
CLOSED: [2022-09-11 Sun 22:05]
*** DONE Corriger PATH pour include java et python
CLOSED: [2022-10-11 Tue 11:46]
https://github.com/NixOS/nixpkgs/pull/191548
Review <2022-10-10 Mon> , corrigé dans la journée
*** DONE Update 4.3.0.0
CLOSED: [2023-04-13 Thu 09:01]
** HOLD Nextflow
*** KILL version script seule
CLOSED: [2023-04-01 Sat 18:29]
Fix pour SGE et nextflow
https://github.com/NixOS/nixpkgs/issues/192396
*** KILL Version avec gradle
CLOSED: [2022-10-09 Sun 22:51]
*** HOLD [[https://github.com/NixOS/nixpkgs/issues/192396][Bug report Version 22.10.6]]
**** Notes
Erreur :
ERROR: Cannot download nextflow required file -- make sure you can connect to the internet
Alternatively you can try to download this file:
    https://www.nextflow.io/releases/v22.10.6/nextflow-22.10.6-all.jar
and save it as:
    .//nix/store/md2b1ah4d7ivj82k8xxap30dmdci00pa-nextflow-22.10.6/bin/.nextflow-wrapped
Dans la mise à jour, il y a la création d'un environnement virtuel qui casse l'exécution de nextflow (besoin de télécharger)
Fix = désactiver
**** KILL Patch NXF_OFFLINE=true
CLOSED: [2023-07-02 Sun 11:02] SCHEDULED: <2023-06-11 Sun>
** TODO Multiqc
SCHEDULED: <2023-08-13 Sun>
** TODO Mutalyzer
SCHEDULED: <2023-08-13 Sun>
** TODO SPIP T2T
SCHEDULED: <2023-08-12 Sat 16:00>
*** TODO PR upstream
SCHEDULED: <2023-08-12 Sat 18:00>
*** TODO Mail R. Lemann
SCHEDULED: <2023-08-12 Sat 18:00>
** TODO VEP :vep:
*** DONE [[https://github.com/NixOS/nixpkgs/pull/185691][BioPerl]]
SCHEDULED: <2022-08-10 Wed>
/Entered on/ [2022-08-09 Tue 10:57]
PR submitted
*** TODO BioDBBBigFile
:PROPERTIES:
:ORDERED:  t
:END:
/Entered on/ [2022-08-10 Wed 14:28]
On utilise la dernière version de kent, donc plus de problème.
PRête à être mergé. Rebase faite<2023-07-02 Sun>
**** DONE Version de kent déjà packagée : forcer version  335
CLOSED: [2023-07-02 Sun 11:20]
***** KILL [[https://github.com/NixOS/nixpkgs/pull/206991][Restore building kent 404]]
CLOSED: [2023-05-06 Sat 17:40]
Review faite <2023-03-26 Sun> , atteinte merge]
Relancé <2023-05-06 Sat>
Kent 446 n'a pas ce problème donc PR inutile
***** DONE [[https://github.com/NixOS/nixpkgs/pull/223411][Ajouter les header to package]] (inc folder)
CLOSED: [2023-05-08 Mon 10:18] SCHEDULED: <2023-05-07 Sun>
Review à faire
https://github.com/NixOS/nixpkgs/pull/223411
Corrigé et plus besoin de la PR précédente
***** KILL [[https://github.com/NixOS/nixpkgs/pull/186462][BioDBBBigFile]] avec ces 2 changements
CLOSED: [2023-07-02 Sun 11:20]
**** KILL Version de kent déjà packagée : 404
CLOSED: [2023-03-27 Mon 16:43]
Compile mais les tests de passent pas
**** DONE Modifier selon PR https://github.com/NixOS/nixpkgs/pull/186462
CLOSED: [2023-07-30 Sun 22:01] SCHEDULED: <2023-07-30 Sun 20:00>
:LOGBOOK:
CLOCK: [2023-07-30 Sun 19:13]--[2023-07-30 Sun 20:50] =>  1:37
:END:
Modification nécessaire pour kent :
- plus de patch
- suppression d'une boucle dans postPatch
On supprime aussi NIX_BUILD_TOP
*** DONE [[https://github.com/NixOS/nixpkgs/pull/186459][BioDBHTS]]
CLOSED: [2023-05-06 Sat 08:49] SCHEDULED: <2023-04-15 Sat>
/Entered on/ [2022-08-10 Wed 14:28]
Correction pour review faites <2022-10-10 Mon>
*** DONE [[https://github.com/NixOS/nixpkgs/pull/186464][BioExtAlign]]
CLOSED: [2022-10-22 Sat 12:43] SCHEDULED: <2022-08-10 Wed>
/Entered on/ [2022-08-10 Wed 14:28]
Review <2022-10-10 Mon>, correction dans la journée.
Correction 2e passe, attente
Impossible de faire marcher les tests Car il ne trouve pas le module Bio::Tools::Align, qui est dans un dossier ailleurs dans le dépôt. Même en compilant tout le dépôt, cela ne fonctionne pas... On skip les tests.
*** TODO VEP
** WAIT [[https://github.com/NixOS/nixpkgs/pull/230394][rtg-tools]] :vcfeval:
Soumis
** WAI

[3.16390]

[2.8221]

l#downloadAlt
- alt = séquences alternatives (utilisables)
- fix = patch (correction ou amélioration)
- random = séquence connue sur un chromosome mais non encore utilisée
** Pipelines prêt-à-l’emploi nextflow
Problème : nécessite singularity ou docker (ou conda)
Potentiellement utilisable avec nix...
** Validation : Quelles données de référence ?
Discussion avec Alexis
- Platinum genomes = génome seul
*** [[https://github.com/genome-in-a-bottle/giab_data_indexes][Genome in a bottle]]
  - NA12878 :
    - Illumina HiSeq Exome : fastq + capture en hg37
    - Illumina TruSeq Exome : bam, pas de capture
    - Exomes en hg37 https://zenodo.org/record/3597727 avec capture
      - HiSeq2000
      - NextSeq 500
      - HiSeq 2500
  - HG002,3,4
    - Illumina Whole Exome  : bam. le kit de capture est "Agilent SureSelect Human All Exon V5 kit" selon [[https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/OsloUniversityHospital_Exome_GATK_jointVC_11242015/README.txt][README]]. On il faut les régions [[https://kb.10xgenomics.com/hc/en-us/articles/115004150923-Where-can-I-find-the-Agilent-Target-BED-files-][selon ce site]]
      Un autre fichier est disponible (capture ???)
    https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/OsloUniversityHospital_Exome_GATK_jointVC_11242015/wex_Agilent_SureSelect_v05_b37.baits.slop50.merged.list
  "target region" +/- 50bp
    testé sur chr311780-312086 : ok
Autres technologies non adaptées au pipeline (vu avec Alexis)
*** [[https://www.illumina.com/platinumgenomes.html][Platinum genome
]] Que du génome « sequenced to 50x depth on a HiSeq 2000 system”
Genome possible
*** 1000 genomes
- intersection des capture + CCDS  [[id:b77e64fa-06a8-4ffa-8b5b-ab3fda684b61][Données brutes exome 1000 Genomes (fastq + capture)]]
- Broad instute : SureSelect human all exon v2 target capture kit : non disponible sur le site d'agilent (V6 ou plus)
*** Zone de capture
GIAB fourni le .bed pour l'exome . INfo : https://support.illumina.com/sequencing/sequencing_kits/nextera-rapid-capture-exome-kit/downloads.html
*** Valider la méthode
- 1000 genomes + SureSelect human all exon v2 target capture kit : non disponible sur le site d'agilent (V6 ou plus)
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2928-9
- GIAB + liftover du fichire de capture en hg38
Ce qui est aussi fait par
https://bcbio-nextgen.readthedocs.io/en/stable/contents/germline_variants.html
Mais avec UCSC liftover
** Centogène
https://www.twistbioscience.com/node/23906
Bed non fourni pour exactement cette capture
On prend https://www.twistbioscience.com/resources/data-files/twist-alliance-vcgs-exome-401mb-bed-files
qui content la majeure partie
* Réunion
** <2023-08-10 Thu> Alexis
Ok pour bloquer le développment d'ici mardi prochain
Dév:
- pipeline jusque VEP en T2T + GRCh38
- ok pour valider spip T2T sur quelques variant => à intégrer au pipeline
- annotation :
  - ok pour mobidetails hg38
  - +OMIM T2T+ non
  - +franklin hg38+ non pour le moment
- métriques (fastq a minima) + rapport multiqc
- optionnel
  - reformater la sortie
- on abandonne
  - XAMScissors ave indel
  - parallélisation haplotype caller
  - spliceai à la vollée
  - pangolin
Test
- GIAB:
  - hg38: ok pour refaire les tests NA12878 avec données cento, sinon ok pour "c'est difficile" sur les 3 fichiers de capture
  - T2T: ok pour faire des tests rapides mais probablement pas assez de temps !
- patient de synthèse : variant cento confirém par sanger seuls
Résultats
- ok pour scale up bwa mem et haplotyecaller
Manuscrit
- validation de méthode : laisser tomber la version actuelle et faire comme strasbourg (cf ngs diag) dans la présentatino
- a envoyé le powerponit avec les références des différsences articles
- ok pour robo4 si résultat
- architecture cible = VM : 78 coeurs 54Go RAUM et 1To espace disque
Passage en production : ok pour présentation rapide du code
* Nixpkgs :nix:
** DONE GATK
CLOSED: [2023-05-06 Sat 08:51]
*** DONE [[https://github.com/NixOS/nixpkgs/pull/185819][Binaire]]
CLOSED: [2022-09-10 Sat 23:53] SCHEDULED: <2022-08-10 Wed>
/Entered on/ [2022-08-09 Tue 10:57]
PR submitted
*** KILL Corriger code pour utiliser source
CLOSED: [2022-09-11 Sun 22:05]
*** DONE Corriger PATH pour include java et python
CLOSED: [2022-10-11 Tue 11:46]
https://github.com/NixOS/nixpkgs/pull/191548
Review <2022-10-10 Mon> , corrigé dans la journée
*** DONE Update 4.3.0.0
CLOSED: [2023-04-13 Thu 09:01]
** HOLD Nextflow
*** KILL version script seule
CLOSED: [2023-04-01 Sat 18:29]
Fix pour SGE et nextflow
https://github.com/NixOS/nixpkgs/issues/192396
*** KILL Version avec gradle
CLOSED: [2022-10-09 Sun 22:51]
*** HOLD [[https://github.com/NixOS/nixpkgs/issues/192396][Bug report Version 22.10.6]]
**** Notes
Erreur :
ERROR: Cannot download nextflow required file -- make sure you can connect to the internet
Alternatively you can try to download this file:
    https://www.nextflow.io/releases/v22.10.6/nextflow-22.10.6-all.jar
and save it as:
    .//nix/store/md2b1ah4d7ivj82k8xxap30dmdci00pa-nextflow-22.10.6/bin/.nextflow-wrapped
Dans la mise à jour, il y a la création d'un environnement virtuel qui casse l'exécution de nextflow (besoin de télécharger)
Fix = désactiver
**** KILL Patch NXF_OFFLINE=true
CLOSED: [2023-07-02 Sun 11:02] SCHEDULED: <2023-06-11 Sun>
** TODO Multiqc
SCHEDULED: <2023-08-13 Sun>
** TODO Mutalyzer
SCHEDULED: <2023-08-13 Sun>
** TODO SPIP T2T
*** DONE PR upstream
CLOSED: [2023-08-12 Sat 18:23] SCHEDULED: <2023-08-12 Sat 18:00>
*** DONE Mail R. Lemann
CLOSED: [2023-08-12 Sat 18:23] SCHEDULED: <2023-08-12 Sat 18:00>
*** TODO Mise à jour packages nix
** TODO VEP :vep:
*** DONE [[https://github.com/NixOS/nixpkgs/pull/185691][BioPerl]]
SCHEDULED: <2022-08-10 Wed>
/Entered on/ [2022-08-09 Tue 10:57]
PR submitted
*** TODO BioDBBBigFile
:PROPERTIES:
:ORDERED:  t
:END:
/Entered on/ [2022-08-10 Wed 14:28]
On utilise la dernière version de kent, donc plus de problème.
PRête à être mergé. Rebase faite<2023-07-02 Sun>
**** DONE Version de kent déjà packagée : forcer version  335
CLOSED: [2023-07-02 Sun 11:20]
***** KILL [[https://github.com/NixOS/nixpkgs/pull/206991][Restore building kent 404]]
CLOSED: [2023-05-06 Sat 17:40]
Review faite <2023-03-26 Sun> , atteinte merge]
Relancé <2023-05-06 Sat>
Kent 446 n'a pas ce problème donc PR inutile
***** DONE [[https://github.com/NixOS/nixpkgs/pull/223411][Ajouter les header to package]] (inc folder)
CLOSED: [2023-05-08 Mon 10:18] SCHEDULED: <2023-05-07 Sun>
Review à faire
https://github.com/NixOS/nixpkgs/pull/223411
Corrigé et plus besoin de la PR précédente
***** KILL [[https://github.com/NixOS/nixpkgs/pull/186462][BioDBBBigFile]] avec ces 2 changements
CLOSED: [2023-07-02 Sun 11:20]
**** KILL Version de kent déjà packagée : 404
CLOSED: [2023-03-27 Mon 16:43]
Compile mais les tests de passent pas
**** DONE Modifier selon PR https://github.com/NixOS/nixpkgs/pull/186462
CLOSED: [2023-07-30 Sun 22:01] SCHEDULED: <2023-07-30 Sun 20:00>
:LOGBOOK:
CLOCK: [2023-07-30 Sun 19:13]--[2023-07-30 Sun 20:50] =>  1:37
:END:
Modification nécessaire pour kent :
- plus de patch
- suppression d'une boucle dans postPatch
On supprime aussi NIX_BUILD_TOP
*** DONE [[https://github.com/NixOS/nixpkgs/pull/186459][BioDBHTS]]
CLOSED: [2023-05-06 Sat 08:49] SCHEDULED: <2023-04-15 Sat>
/Entered on/ [2022-08-10 Wed 14:28]
Correction pour review faites <2022-10-10 Mon>
*** DONE [[https://github.com/NixOS/nixpkgs/pull/186464][BioExtAlign]]
CLOSED: [2022-10-22 Sat 12:43] SCHEDULED: <2022-08-10 Wed>
/Entered on/ [2022-08-10 Wed 14:28]
Review <2022-10-10 Mon>, correction dans la journée.
Correction 2e passe, attente
Impossible de faire marcher les tests Car il ne trouve pas le module Bio::Tools::Align, qui est dans un dossier ailleurs dans le dépôt. Même en compilant tout le dépôt, cela ne fonctionne pas... On skip les tests.
*** TODO VEP
** WAIT [[https://github.com/NixOS/nixpkgs/pull/230394][rtg-tools]] :vcfeval:
Soumis
** WAI

Replacement in projects/bisonex.org at line 9 [4.35]

B:BD[5.14811] → [5.14811:15038]

B:BD[5.15038] → [2.8449:16414]

rner les tests.
Il faut remplace bin/test_haplotypes par test_haplotypes dans src/sh/run_tests.sh
#+begin_src sh
 HGREF=../genome/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta HCDIR=~/anaconda3/envs/py2/bin bash s
rc/sh/run_tests.sh
#+end_src
Echec:
test_haplotypes: /opt/conda/conda-bld/work/hap.py-0.3.7/src/c++/lib/tools/Fasta.cpp:81: MMappedFastaFile::MMappedFastaFile(const string&): Assertion `fd != -1' failed.
unknown location(0): fatal error in "testVariantPrimitiveSplitter": signal: SIGABRT (application abort requested)
/opt/conda/conda-bld/work/hap.py-0.3.7/src/c++/test/test_align.cpp(298): last checkpoint
******** Chr21
HGREF=../genome/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta hap.py        example/happy/PG_NA12878_chr21.vcf.gz       example/happy/NA12878_chr21.vcf.gz       -f example/happy/PG_Conf_chr21.bed.gz       -o test
******* Helios
échec
** TODO T2T :T2T:
Toutes les ressourcs sont décrites ici
https://github.com/marbl/CHM13
Détails sur le pipeline
https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hub_3267197_GCA_009914755.4&c=CP068277.2&g=hub_3267197_hgLiftOver
*** Liftover pipelines
:PROPERTIES:
:ID:       d2280207-3f65-4a31-a291-41fa9a9658c2
:END:
Contient les chain files
*** DONE Alignement
CLOSED: [2023-06-26 Mon 19:42]
NXF_OPTS=-D"user.name=${USER}" nextflow run main.nf -profile standard,helios  --input="/Work/Groups/bisonex/data/giab/*_R{1,2}_001.fastq.gz" --id=NA12878-T2T -bg
SCHEDULED: <2023-06-14 Wed>
*** DONE Haplotypecaller
CLOSED: [2023-06-26 Mon 19:42] SCHEDULED: <2023-06-15 Thu>
*** DONE Faire fonctionner le filtre technical variant
CLOSED: [2023-08-03 Thu 14:24] SCHEDULED: <2023-08-03 Wed 10:30>
*** DONE Annotation vep seule
CLOSED: [2023-08-05 Sat 08:59] SCHEDULED: <2023-08-05 Sat>
T2T n'a pas
- de version merged
- polyphen
- gnomAD
On désactive l'annotation spip pour le moment
*** DONE Générer la base de donnée spip :spip:
CLOSED: [2023-08-09 Wed 21:41] SCHEDULED: <2023-08-03 Thu 11:30>
**** KILL Vérifier la génération du transcriptome en hg38: checksum différent
CLOSED: [2023-08-09 Wed 21:41]
- [X] Nettoyer et vérifier sur hg38 avec ediff les RData : différent
- [X] Sinon, ne pas nettoyer et générer: idem
**** DONE Récupérer ncbi RefSeq curated
CLOSED: [2023-08-07 Mon 22:59] SCHEDULED: <2023-08-06 Sun>
.txt sur UCSC mais pas en T2T: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
Format: https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=1173061381_UepaHnvaOKFZKMOV4o7DtcNUHGVa&hgta_doSchemaDb=chlSab2&hgta_doSchemaTable=ncbiRefSeqCurated
Ancient format vs nouveau
|  1 | bin          |  1 | chrom        |
|  2 | name         |  2 | chromStart   |
|  3 | chrom        |  3 | chromEnd     |
|  4 | strand       |  4 | name         |
|  5 | txStart      |  5 | score        |
|  6 | txEnd        |  6 | strand       |
|  7 | cdsStart     |  7 | thickStart   |
|  8 | cdsEnd       |  8 | thickEnd     |
|  9 | exonCount    |  9 | reserved     |
| 10 | exonStarts   | 10 | blockCount   |
| 11 | exonEnds     | 11 | blockSizes   |
| 12 | score        | 12 | chromStarts  |
| 13 | name2        | 13 | name2        |
| 14 | cdsStartStat | 14 | cdsStartStat |
| 15 | cdsEndStat   | 15 | cdsEndStat   |
| 16 | exonFrames   | 16 | exonFrames   |
|    |              | 17 | type         |
|    |              | 18 | geneName     |
|    |              | 19 | geneName2    |
|    |              | 20 | geneType     |
En T2T, seulement au format bigBed : https://hgdownload.soe.ucsc.edu/gbdb/hs1/ncbiRefSeq/
Il y a un exécutable pour convertir en bed : http://hgdownload.soe.ucsc.edu/admin/exe/
Sous gentoo, il faut instaler mit-krb5 (pour libkrb5)
#+begin_src
./bigBedToBed ncbiRefSeqCurated.bb ncbiRefSeqCurated.bed
#+end_src
Exemple:
chr1    7505    13582   NR_182076.1     0       -       13582   13582   0       2       5477,138,       0,5939, LOC127239154    none    none    -1,-1,          NR_182076.1     LOC127239154
Dans R:
   V1        V2   V3 V4    V5    V6    V7    V8 V9                V10
1 585 NR_046018 chr1  + 11873 14409 14409 14409  3 11873,12612,13220,
                 V11 V12     V13  V14  V15       V16           V17         V18
1 12227,12721,14409,   0 DDX11L1 none none -1,-1,-1, 354,109,1189, 0,739,1347,
Ne pas oublier les headers car ils sont dans un ordre différent:
Colonnes en GRGh38 =
3, 5, 6, 2, 12, 4, 7,  8, 12, 9, 17, 18, 13
Correspondance en T2T
1, 7, 8, 4, 5,  6, 14, 15, 5, ?,  ?,  ?, 13
En fait, il suffit d'avoir
- le gène
- le début du transcrit
- la fin du transcrit
- le brin
  pour générer
***** KILL Tester correspondance partielle ?
CLOSED: [2023-08-07 Mon 22:58]
pas de CDS et pas de colonne 17 et 18
seules les colonnes (dans la nouvelle dataframe) 10,11,12 causent problèmes (9,17,18 dans les ancienne)
NB: on peut retrouver le nombre d'exons colonnes 9 à partir de la lons
***** DONE Correspondance totale
CLOSED: [2023-08-07 Mon 22:59]
> dataRefSeq[1,]
    V1    V2    V3        V4 V5 V6    V7    V8 V9 V10           V11         V12
1 chr1 11873 14409 NR_046018  0  + 14409 14409  0   3 354,109,1189, 0,739,1347,
      V13
1 DDX11L1
> source("pkgs/getRefSeqDatabaseT2T.r")
Use the URL: http://hgdownload.cse.ucsc.edu/goldenPath/
read files...
> dataRefSeq[1,]
    V1   V2    V3        V4 V5 V6    V7    V8 V5.1 V10       V11     V12
1 chr1 7505 13582 NR_182076  0  - 13582 13582    0   2 5477,138, 0,5939,
           V13
1 LOC127239154
*** TODO Inclure génération refseq + transcriptom T2T dans dérivation nix :spip:
SCHEDULED: <2023-08-12 Sat 15:00>
**** TODO [#A] Tester nouvelle dérivation
SCHEDULED: <2023-08-12 Sat 15:00>
*** DONE Vérifier annotation SPIP sur variants confirmé
CLOSED: [2023-08-10 Thu 23:16] SCHEDULED: <2023-08-09 Wed>
**** DONE 5 variants patho tirés de l'article princips
CLOSED: [2023-08-10 Thu 23:00]
On trié par SQUIRLS décroissant
#+begin_src sh
varID
NM_000051:c.2251-10T>G
NM_000267:c.889-12T>A
NM_000059:c.8488-9T>G
NM_000249:c.589-10T>A
NM_000249:c.791-7T>A
#+end_src
***** DONE En hg38
CLOSED: [2023-08-09 Wed 22:01]
#+begin_src
spip --input test-spip.txt --output test-spip.out --GenomeAssenbly hg38 --threads 1 --maxLines 1000
#+end_src
#+RESULTS:
| varID                  | Interpretation | InterConfident              | SPiPscore | strand |    gNomen | varType      | ntChange | ExonInfo  | exonSize | transcript | gene  | NearestSS | DistSS | RegType    | SPiCEproba | SPiCEinter_2thr | deltaMES | BP  | mutInPBarea | deltaESRscore | posCryptMut | sstypeCryptMut | probaCryptMut | classProbaCryptMut | nearestSStoCrypt | nearestPosSStoCrypt | nearestDistSStoCrypt | posCryptWT | probaCryptWT | classProbaCryptWT | posSSPhysio | probaSSPhysio | classProbaSSPhysio | probaSSPhysioMut | classProbaSSPhysioMut |
| NM_000051:c.2251-10T>G | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.986 | +      | 108257471 | substitution | T>G      | Intron 14 |     1140 | NM_000051  | ATM   | acceptor  |    -10 | IntronCons |          1 | high            |        0 | 0No |          10 |     108257471 | Acc         |    0.024836003 | No            | Acc                |        108257480 |                 -10 |                    0 |          0 | No           |         108257480 | 0.006489079 | No            |     0.000004368542 | No               |                       |
| NM_000267:c.889-12T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     1.000 | +      |  31200410 | substitution | T>A      | Intron 8  |    17756 | NM_000267  | NF1   | acceptor  |    -12 | IntronCons |          1 | high            |        0 | 0No |          10 |      31200411 | Acc         |    0.009082899 | No            | Acc                |         31200421 |                 -11 |                    0 |          0 | No           |          31200421 | 0.005160854 | No            |     0.000003718518 | No               |                       |
| NM_000059:c.8488-9T>G  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.994 | +      |  32370947 | substitution | T>G      | Intron 19 |      398 | NM_000059  | BRCA2 | acceptor  |

[5.14811]

[2.16414]

rner les tests.
Il faut remplace bin/test_haplotypes par test_haplotypes dans src/sh/run_tests.sh
#+begin_src sh
 HGREF=../genome/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta HCDIR=~/anaconda3/envs/py2/bin bash src/sh/run_tests.sh
#+end_src
Echec:
test_haplotypes: /opt/conda/conda-bld/work/hap.py-0.3.7/src/c++/lib/tools/Fasta.cpp:81: MMappedFastaFile::MMappedFastaFile(const string&): Assertion `fd != -1' failed.
unknown location(0): fatal error in "testVariantPrimitiveSplitter": signal: SIGABRT (application abort requested)
/opt/conda/conda-bld/work/hap.py-0.3.7/src/c++/test/test_align.cpp(298): last checkpoint
******** Chr21
HGREF=../genome/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta hap.py        example/happy/PG_NA12878_chr21.vcf.gz       example/happy/NA12878_chr21.vcf.gz       -f example/happy/PG_Conf_chr21.bed.gz       -o test
******* Helios
échec
** TODO T2T :T2T:
Toutes les ressourcs sont décrites ici
https://github.com/marbl/CHM13
Détails sur le pipeline
https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hub_3267197_GCA_009914755.4&c=CP068277.2&g=hub_3267197_hgLiftOver
*** Liftover pipelines
:PROPERTIES:
:ID:       d2280207-3f65-4a31-a291-41fa9a9658c2
:END:
Contient les chain files
*** DONE Alignement
CLOSED: [2023-06-26 Mon 19:42]
NXF_OPTS=-D"user.name=${USER}" nextflow run main.nf -profile standard,helios  --input="/Work/Groups/bisonex/data/giab/*_R{1,2}_001.fastq.gz" --id=NA12878-T2T -bg
SCHEDULED: <2023-06-14 Wed>
*** DONE Haplotypecaller
CLOSED: [2023-06-26 Mon 19:42] SCHEDULED: <2023-06-15 Thu>
*** DONE Faire fonctionner le filtre technical variant
CLOSED: [2023-08-03 Thu 14:24] SCHEDULED: <2023-08-03 Wed 10:30>
*** DONE Annotation vep seule
CLOSED: [2023-08-05 Sat 08:59] SCHEDULED: <2023-08-05 Sat>
T2T n'a pas
- de version merged
- polyphen
- gnomAD
On désactive l'annotation spip pour le moment
*** DONE Générer la base de donnée spip :spip:
CLOSED: [2023-08-09 Wed 21:41] SCHEDULED: <2023-08-03 Thu 11:30>
**** KILL Vérifier la génération du transcriptome en hg38: checksum différent
CLOSED: [2023-08-09 Wed 21:41]
- [X] Nettoyer et vérifier sur hg38 avec ediff les RData : différent
- [X] Sinon, ne pas nettoyer et générer: idem
**** DONE Récupérer ncbi RefSeq curated
CLOSED: [2023-08-07 Mon 22:59] SCHEDULED: <2023-08-06 Sun>
.txt sur UCSC mais pas en T2T: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
Format: https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=1173061381_UepaHnvaOKFZKMOV4o7DtcNUHGVa&hgta_doSchemaDb=chlSab2&hgta_doSchemaTable=ncbiRefSeqCurated
Ancient format vs nouveau
|  1 | bin          |  1 | chrom        |
|  2 | name         |  2 | chromStart   |
|  3 | chrom        |  3 | chromEnd     |
|  4 | strand       |  4 | name         |
|  5 | txStart      |  5 | score        |
|  6 | txEnd        |  6 | strand       |
|  7 | cdsStart     |  7 | thickStart   |
|  8 | cdsEnd       |  8 | thickEnd     |
|  9 | exonCount    |  9 | reserved     |
| 10 | exonStarts   | 10 | blockCount   |
| 11 | exonEnds     | 11 | blockSizes   |
| 12 | score        | 12 | chromStarts  |
| 13 | name2        | 13 | name2        |
| 14 | cdsStartStat | 14 | cdsStartStat |
| 15 | cdsEndStat   | 15 | cdsEndStat   |
| 16 | exonFrames   | 16 | exonFrames   |
|    |              | 17 | type         |
|    |              | 18 | geneName     |
|    |              | 19 | geneName2    |
|    |              | 20 | geneType     |
En T2T, seulement au format bigBed : https://hgdownload.soe.ucsc.edu/gbdb/hs1/ncbiRefSeq/
Il y a un exécutable pour convertir en bed : http://hgdownload.soe.ucsc.edu/admin/exe/
Sous gentoo, il faut instaler mit-krb5 (pour libkrb5)
#+begin_src
./bigBedToBed ncbiRefSeqCurated.bb ncbiRefSeqCurated.bed
#+end_src
Exemple:
chr1    7505    13582   NR_182076.1     0       -       13582   13582   0       2       5477,138,       0,5939, LOC127239154    none    none    -1,-1,          NR_182076.1     LOC127239154
Dans R:
   V1        V2   V3 V4    V5    V6    V7    V8 V9                V10
1 585 NR_046018 chr1  + 11873 14409 14409 14409  3 11873,12612,13220,
                 V11 V12     V13  V14  V15       V16           V17         V18
1 12227,12721,14409,   0 DDX11L1 none none -1,-1,-1, 354,109,1189, 0,739,1347,
Ne pas oublier les headers car ils sont dans un ordre différent:
Colonnes en GRGh38 =
3, 5, 6, 2, 12, 4, 7,  8, 12, 9, 17, 18, 13
Correspondance en T2T
1, 7, 8, 4, 5,  6, 14, 15, 5, ?,  ?,  ?, 13
En fait, il suffit d'avoir
- le gène
- le début du transcrit
- la fin du transcrit
- le brin
  pour générer
***** KILL Tester correspondance partielle ?
CLOSED: [2023-08-07 Mon 22:58]
pas de CDS et pas de colonne 17 et 18
seules les colonnes (dans la nouvelle dataframe) 10,11,12 causent problèmes (9,17,18 dans les ancienne)
NB: on peut retrouver le nombre d'exons colonnes 9 à partir de la lons
***** DONE Correspondance totale
CLOSED: [2023-08-07 Mon 22:59]
> dataRefSeq[1,]
    V1    V2    V3        V4 V5 V6    V7    V8 V9 V10           V11         V12
1 chr1 11873 14409 NR_046018  0  + 14409 14409  0   3 354,109,1189, 0,739,1347,
      V13
1 DDX11L1
> source("pkgs/getRefSeqDatabaseT2T.r")
Use the URL: http://hgdownload.cse.ucsc.edu/goldenPath/
read files...
> dataRefSeq[1,]
    V1   V2    V3        V4 V5 V6    V7    V8 V5.1 V10       V11     V12
1 chr1 7505 13582 NR_182076  0  - 13582 13582    0   2 5477,138, 0,5939,
           V13
1 LOC127239154
*** DONE Inclure génération refseq + transcriptom T2T dans dérivation nix :spip:
CLOSED: [2023-08-12 Sat 18:08] SCHEDULED: <2023-08-12 Sat 15:00>
**** DONE [#A] Tester nouvelle dérivation
CLOSED: [2023-08-12 Sat 18:08] SCHEDULED: <2023-08-12 Sat 15:00>
***** DONE En hg38
CLOSED: [2023-08-12 Sat 17:59]
test-spip-hg38.txt
varID
NM_000051:c.2251-10T>G
NM_000267:c.889-12T>A
NM_000059:c.8488-9T>G
NM_000249:c.589-10T>A
NM_000249:c.791-7T>A
#+begin_src
❯ ../result/bin/spip -I test-spip-hg38.txt -O test-spip-hg38.out -g hg38
#+end_src
#+RESULTS:
| varID                  | Interpretation | InterConfident | SPiPscore | strand | gNomen | varType | ntChange | ExonInfo | exonSize | transcript |  gene | NearestSS |    DistSS | RegType      | SPiCEproba | SPiCEinter_2thr | deltaMES |    BP | mutInPBarea | deltaESRscore | posCryptMut | sstypeCryptMut | probaCryptMut | classProbaCryptMut | nearestSStoCrypt | nearestPosSStoCrypt | nearestDistSStoCrypt | posCryptWT | probaCryptWT | classProbaCryptWT | posSSPhysio | probaSSPhysio | classProbaSSPhysio | probaSSPhysioMut | classProbaSSPhysioMut |   |   |    |           |             |    |                |    |
| NM_000051:c.2251-10T>G | Alter          | by             | SPiCE     |  98.41 | %      | [91.47  | %        | -        |    99.96 | %]         | 0.986 | +         | 108257471 | substitution | T>G        | Intron          |       14 |  1140 | NM_000051   | ATM           | acceptor    |            -10 | IntronCons    |                  1 | high             |                   0 | 0No                  |         10 |    108257471 | Acc               | 0.024836003 | No            | Acc                |        108257480 |                   -10 | 0 | 0 | No | 108257480 | 0.006489079 | No | 0.000004368542 | No |
| NM_000267:c.889-12T>A  | Alter          | by             | SPiCE     |  98.41 | %      | [91.47  | %        | -        |    99.96 | %]         | 1.000 | +         |  31200410 | substitution | T>A        | Intron          |        8 | 17756 | NM_000267   | NF1           | acceptor    |            -12 | IntronCons    |                  1 | high             |                   0 | 0No                  |         10 |     31200411 | Acc               | 0.009082899 | No            | Acc                |         31200421 |                   -11 | 0 | 0 | No |  31200421 | 0.005160854 | No | 0.000003718518 | No |
| NM_000059:c.8488-9T>G  | Alter          | by             | SPiCE     |  98.41 | %      | [91.47  | %        | -        |    99.96 | %]         | 0.994 | +         |  32370947 | substitution | T>G        | Intron          |       19 |   398 | NM_000059   | BRCA2         | acceptor    |             -9 | IntronCons    |                  1 | high             |                   0 | 0No                  |         10 |     32370947 | Acc               | 0.004449623 | No            | Acc                |         32370955 |                    -9 | 0 | 0 | No |  32370955 | 0.005060308 | No | 0.000005609419 | No |
| NM_000249:c.589-10T>A  | Alter          | by             | SPiCE     |  98.41 | %      | [91.47  | %        | -        |    99.96 | %]         | 0.978 | +         |  37012001 | substitution | T>A        | Intron          |        7 |   148 | NM_000249   | MLH1          | acceptor    |            -10 | IntronCons    |                  1 | high             |                   0 | 0No                  |         10 |     37012002 | Acc               | 0.009529819 | No            | Acc                |         37012010 |                    -9 | 0 | 0 | No |  37012010 | 0.028437574 | No | 0.000009275960 | No |
| NM_000249:c.791-7T>A   | Alter          | by             | SPiCE     |  98.41 | %      | [91.47  | %        | -        |    99.96 | %]         | 0.988 | +         |  37017499 | substitution | T>A        | Intron          |        9 |  2961 | NM_000249   | MLH1          | acceptor    |             -7 | IntronCons    |                  1 | high             |                   0 | 0No                  |         10 |     37017500 | Acc               | 0.015564917 | No            | Acc                |         37017505 |                    -6 | 0 | 0 | No |  37017505 | 0.023995855 | No | 0.000022606476 | No |
|                        |                |                |           |        |        |         |          |          |          |            |       |           |           |              |            |                 |          |       |             |               |             |                |               |                    |                  |                     |                      |            |              |                   |             |               |                    |                  |                       |   |   |    |           |             |    |                |    |
|                        |                |                |           |        |        |         |          |          |          |            |       |           |           |              |            |                 |          |       |             |               |             |                |               |                    |                  |                     |                      |            |              |                   |             |               |                    |                  |                       |   |   |    |           |             |    |                |    |
***** DONE En T2T
CLOSED: [2023-08-12 Sat 18:08]
****** DONE Sur  1 variant avec score 35.01%: ok
CLOSED: [2023-08-12 Sat 18:05]
##fileformat=VCFv4.0
##assembly=CHM18v2.0/hs1
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
chr10	89894645	lol	A	G	.	.	.
 #+begin_src
 ../result/bin/spip -I test-spip-T2T.vcf -O test-spip-T2T.out -g hs1
 #+end_src
#+RESULTS:
| CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	varID	Interpretation	InterConfident	SPiPscore	strand	gNomen	varType	ntChange	ExonInfo	exonSize	transcript	gene	NearestSS	DistSS	RegType	SPiCEproba	SPiCEinter_2thr	deltaMES	BP	mutInPBarea	deltaESRscore	posCryptMut	sstypeCryptMut	probaCryptMut	classProbaCryptMut	nearestSStoCrypt	nearestPosSStoCrypt	nearestDistSStoCrypt	posCryptWT	probaCryptWT	classProbaCryptWT	posSSPhysio	probaSSPhysio	classProbaSSPhysio	probaSSPhysioMut	classProbaSSPhysioMut |
| chr10	89894645	lol	A	G	.	.	.	NM_000043:g.89894645:A>G	Alter ESR	35.81 % [28.11 % - 44.1 %]	0.288	+	89894645	substitution	A>G	Exon 6	  63	NM_000043	FAS	acceptor	  8	ExonESR	0	Outside SPiCE Interpretation	0	0	No	-1.67753	89894644	Acc	0.0000003317384	No	Acc	89894637	7	89894644	0.0000002205815	No	89894637	0.02545572	No	0.02545572	No |
| chr10	89894645	lol	A	G	.	.	.	NM_001320619:g.89894645:A>G	Alter ESR	35.81 % [28.11 % - 44.1 %]	0.288	+	89894645	substitution	A>G	Exon 6	  63	NM_001320619	FAS	acceptor	  8	ExonESR	0	Outside SPiCE Interpretation	0	0	No	-1.67753	89894644	Acc	0.0000003317384	No	Acc	89894637	7	89894644	0.0000002205815	No	89894637	0.02545572	No	0.02545572	No |
| chr10	89894645	lol	A	G	.	.	.	NM_152871:g.89894645:A>G	NTR	00 % [00 % - 00.92 %]	0.000	+	89894645	substitution	A>G	Intron 5	1398	NM_152871	FAS	donor	160	DeepIntron	0	Outside SPiCE Interpretation	0	0	No	10.00000	89894644	Don	0.0001360257829	No	Don	89894485	159	0	0.0000000000000	No	89894485	0.07177992	Yes	0.07177992	Yes |
| chr10	89894645	lol	A	G	.	.	.	NM_152872:g.89894645:A>G	Alter ESR	35.81 % [28.11 % - 44.1 %]	0.288	+	89894645	substitution	A>G	Exon 6	  63	NM_152872	FAS	acceptor	  8	ExonESR	0	Outside SPiCE Interpretation	0	0	No	-1.67753	89894644	Acc	0.0000003317384	No	Acc	89894637	7	89894644	0.0000002205815	No	89894637	0.02545572	No	0.02545572	No |
| chr10	89894645	lol	A	G	.	.	.	NR_028033:g.89894645:A>G	NTR	00 % [00 % - 00.92 %]	0.000	+	89894645	substitution	A>G	Intron 4	1398	NR_028033	FAS	donor	160	DeepIntron	0	Outside SPiCE Interpretation	0	0	No	10.00000	89894644	Don	0.0001360257829	No	Don	89894485	159	0	0.0000000000000	No	89894485	0.07177992	Yes	0.07177992	Yes |
| chr10	89894645	lol	A	G	.	.	.	NR_028034:g.89894645:A>G	NTR	00 % [00 % - 00.92 %]	0.000	+	89894645	substitution	A>G	Intron 3	1398	NR_028034	FAS	donor	160	DeepIntron	0	Outside SPiCE Interpretation	0	0	No	10.00000	89894644	Don	0.0001360257829	No	Don	89894485	159	0	0.0000000000000	No	89894485	0.07177992	Yes	0.07177992	Yes |
| chr10	89894645	lol	A	G	.	.	.	NR_028035:g.89894645:A>G	Alter ESR	35.81 % [28.11 % - 44.1 %]	0.288	+	89894645	substitution	A>G	Exon 4	  63	NR_028035	FAS	acceptor	  8	ExonESR	0	Outside SPiCE Interpretation	0	0	No	-1.67753	89894644	Acc	0.0000003317384	No	Acc	89894637	7	89894644	0.0000002205815	No	89894637	0.02545572	No	0.02545572	No |
| chr10	89894645	lol	A	G	.	.	.	NR_028036:g.89894645:A>G	Alter ESR	35.81 % [28.11 % - 44.1 %]	0.288	+	89894645	substitution	A>G	Exon 5	  63	NR_028036	FAS	acceptor	  8	ExonESR	0	Outside SPiCE Interpretation	0	0	No	-1.67753	89894644	Acc	0.0000003317384	No	Acc	89894637	7	89894644	0.0000002205815	No	89894637	0.02545572	No	0.02545572	No |
| chr10	89894645	lol	A	G	.	.	.	NR_135313:g.89894645:A>G	Alter ESR	35.81 % [28.11 % - 44.1 %]	0.288	+	89894645	substitution	A>G	Exon 5	  63	NR_135313	FAS	acceptor	  8	ExonESR	0	Outside SPiCE Interpretation	0	0	No	-1.67753	89894644	Acc	0.0000003317384	No	Acc	89894637	7	89894644	0.0000002205815	No	89894637	0.02545572	No	0.02545572	No |
| chr10	89894645	lol	A	G	.	.	.	NM_001410956:g.89894645:A>G	Alter ESR	35.81 % [28.11 % - 44.1 %]	0.288	+	89894645	substitution	A>G	Exon 6	  63	NM_001410956	FAS	acceptor	  8	ExonESR	0	Outside SPiCE Interpretation	0	0	No	-1.67753	89894644	Acc	0.0000003317384	No	Acc	89894637	7	89894644	0.0000002205815	No	89894637	0.02545572	No	0.02545572	No |
| chr10	89894645	lol	A	G	.	.	.	NR_135314:g.89894645:A>G	Alter ESR	35.81 % [28.11 % - 44.1 %]	0.288	+	89894645	substitution	A>G	Exon 6	  63	NR_135314	FAS	acceptor	  8	ExonESR	0	Outside SPiCE Interpretation	0	0	No	-1.67753	89894644	Acc	0.0000003317384	No	Acc	89894637	7	89894644	0.0000002205815	No	89894637	0.02545572	No	0.02545572	No |
| chr10	89894645	lol	A	G	.	.	.	NR_135315:g.89894645:A>G	Alter ESR	35.81 % [28.11 % - 44.1 %]	0.288	+	89894645	substitution	A>G	Exon 4	  63	NR_135315	FAS	acceptor	  8	ExonESR	0	Outside SPiCE Interpretation	0	0	No	-1.67753	89894644	Acc	0.0000003317384	No	Acc	89894637	7	89894644	0.0000002205815	No	89894637	0.02545572	No	0.02545572	No |
|                                                                                                                      |
****** DONE 5 variants patho
CLOSED: [2023-08-12 Sat 18:08]
##fileformat=VCFv4.0
##assembly=CHM13v2.0/hs1
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
chr11	108264994	lol	T	G	.	.	.
chr17	32146124	lol	T	A	.	.	.
chr3	31588185	lol	T	G	.	.	.
chr3	37013346	lol	T	A	.	.	.
chr3	37018844	lol	T	A	.	.	.
 #+begin_src
 ../result/bin/spip -I test-spip-T2T.vcf -O test-spip-T2T.out -g hs1
 #+end_src
 #+RESULTS:
| CHROM |       POS | ID  | REF | ALT | QUAL | FILTER | INFO | varID                        | Interpretation | InterConfident              | SPiPscore | strand |    gNomen | varType      | ntChange | ExonInfo  | exonSize | transcript   | gene  | NearestSS | DistSS | RegType    | SPiCEproba | SPiCEinter_2thr              | deltaMES | BP | mutInPBarea | deltaESRscore | posCryptMut | sstypeCryptMut |    probaCryptMut | classProbaCryptMut | nearestSStoCrypt | nearestPosSStoCrypt | nearestDistSStoCrypt | posCryptWT |     probaCryptWT | classProbaCryptWT | posSSPhysio | probaSSPhysio | classProbaSSPhysio | probaSSPhysioMut | classProbaSSPhysioMut |
| chr11 | 108264994 | lol | T   | G   | .    | .      | .    | NM_000051:g.108264994:T>G    | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.986 | +      | 108264994 | substitution | T>G      | Intron 14 |     1140 | NM_000051    | ATM   | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |   108264994 | Acc            | 0.02483600258856 | No                 | Acc              |           108265003 |                  -10 |          0 | 0.00000000000000 | No                |   108265003 |   0.006489079 | No                 |   0.000004368542 | No                    |
| chr11 | 108264994 | lol | T   | G   | .    | .      | .    | NM_001351834:g.108264994:T>G | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.986 | +      | 108264994 | substitution | T>G      | Intron 15 |     1140 | NM_001351834 | ATM   | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |   108264994 | Acc            | 0.02483600258856 | No                 | Acc              |           108265003 |                  -10 |          0 | 0.00000000000000 | No                |   108265003 |   0.006489079 | No                 |   0.000004368542 | No                    |
| chr17 |  32146124 | lol | T   | A   | .    | .      | .    | NM_000267:g.32146124:T>A     | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     1.000 | +      |  32146124 | substitution | T>A      | Intron 8  |    17755 | NM_000267    | NF1   | acceptor  |    -12 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    32146125 | Acc            | 0.00908289924996 | No                 | Acc              |            32146135 |                  -11 |          0 | 0.00000000000000 | No                |    32146135 |   0.005160854 | No                 |   0.000003718518 | No                    |
| chr17 |  32146124 | lol | T   | A   | .    | .      | .    | NM_001128147:g.32146124:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     1.000 | +      |  32146124 | substitution | T>A      | Intron 8  |    17755 | NM_001128147 | NF1   | acceptor  |    -12 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    32146125 | Acc            | 0.00908289924996 | No                 | Acc              |            32146135 |                  -11 |          0 | 0.00000000000000 | No                |    32146135 |   0.005160854 | No                 |   0.000003718518 | No                    |
| chr17 |  32146124 | lol | T   | A   | .    | .      | .    | NM_001042492:g.32146124:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     1.000 | +      |  32146124 | substitution | T>A      | Intron 8  |    17755 | NM_001042492 | NF1   | acceptor  |    -12 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    32146125 | Acc            | 0.00908289924996 | No                 | Acc              |            32146135 |                  -11 |          0 | 0.00000000000000 | No                |    32146135 |   0.005160854 | No                 |   0.000003718518 | No                    |
| chr3  |  31588185 | lol | T   | G   | .    | .      | .    | NM_178862:g.31588185:T>G     | NTR            | 00 % [00 % - 00.92 %]       |     0.000 | +      |  31588185 | substitution | T>G      | Intron 3  |    16710 | NM_178862    | STT3B | donor     |   5663 | DeepIntron |          0 | Outside SPiCE Interpretation |        0 |  0 | No          |            10 |    31588184 | Don            | 0.00000002308527 | No                 | Don              |            31582522 |                 5662 |   31588181 | 0.00000000129731 | No                |    31582522 |   0.071835522 | Yes                |   0.071835521718 | Yes                   |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_000249:g.37013346:T>A     | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 7  |      148 | NM_000249    | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001167617:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 7  |      148 | NM_001167617 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001167618:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 7  |      148 | NM_001167618 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001167619:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 6  |      148 | NM_001167619 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001258271:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 7  |      148 | NM_001258271 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001258273:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 6  |      148 | NM_001258273 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001258274:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 8  |      148 | NM_001258274 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001354615:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 6  |      148 | NM_001354615 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001354616:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 6  |      148 | NM_001354616 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001354617:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 7  |      148 | NM_001354617 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001354618:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 7  |      148 | NM_001354618 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001354619:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 8  |      148 | NM_001354619 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001354620:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 7  |      148 | NM_001354620 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001354621:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 7  |      148 | NM_001354621 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001354622:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 7  |      148 | NM_001354622 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001354623:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 6  |      148 | NM_001354623 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001354624:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 7  |      148 | NM_001354624 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001354625:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 6  |      148 | NM_001354625 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001354626:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 7  |      148 | NM_001354626 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001354627:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 7  |      148 | NM_001354627 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001354628:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 7  |      148 | NM_001354628 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001354629:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 6  |      148 | NM_001354629 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37013346 | lol | T   | A   | .    | .      | .    | NM_001354630:g.37013346:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.978 | +      |  37013346 | substitution | T>A      | Intron 7  |      148 | NM_001354630 | MLH1  | acceptor  |    -10 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37013347 | Acc            | 0.00952981867149 | No                 | Acc              |            37013355 |                   -9 |          0 | 0.00000000000000 | No                |    37013355 |   0.028437574 | No                 |   0.000009275960 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_000249:g.37018844:T>A     | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.988 | +      |  37018844 | substitution | T>A      | Intron 9  |     2961 | NM_000249    | MLH1  | acceptor  |     -7 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37018850 |                   -6 |          0 | 0.00000000000000 | No                |    37018850 |   0.023995855 | No                 |   0.000022606476 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001167617:g.37018844:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.988 | +      |  37018844 | substitution | T>A      | Intron 9  |     2961 | NM_001167617 | MLH1  | acceptor  |     -7 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37018850 |                   -6 |          0 | 0.00000000000000 | No                |    37018850 |   0.023995855 | No                 |   0.000022606476 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001167618:g.37018844:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.988 | +      |  37018844 | substitution | T>A      | Intron 9  |     2961 | NM_001167618 | MLH1  | acceptor  |     -7 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37018850 |                   -6 |          0 | 0.00000000000000 | No                |    37018850 |   0.023995855 | No                 |   0.000022606476 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001167619:g.37018844:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.988 | +      |  37018844 | substitution | T>A      | Intron 8  |     2961 | NM_001167619 | MLH1  | acceptor  |     -7 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37018850 |                   -6 |          0 | 0.00000000000000 | No                |    37018850 |   0.023995855 | No                 |   0.000022606476 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001258271:g.37018844:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.988 | +      |  37018844 | substitution | T>A      | Intron 9  |     2961 | NM_001258271 | MLH1  | acceptor  |     -7 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37018850 |                   -6 |          0 | 0.00000000000000 | No                |    37018850 |   0.023995855 | No                 |   0.000022606476 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001258273:g.37018844:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.988 | +      |  37018844 | substitution | T>A      | Intron 8  |     2961 | NM_001258273 | MLH1  | acceptor  |     -7 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37018850 |                   -6 |          0 | 0.00000000000000 | No                |    37018850 |   0.023995855 | No                 |   0.000022606476 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001258274:g.37018844:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.988 | +      |  37018844 | substitution | T>A      | Intron 10 |     2961 | NM_001258274 | MLH1  | acceptor  |     -7 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37018850 |                   -6 |          0 | 0.00000000000000 | No                |    37018850 |   0.023995855 | No                 |   0.000022606476 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001354615:g.37018844:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.988 | +      |  37018844 | substitution | T>A      | Intron 8  |     2961 | NM_001354615 | MLH1  | acceptor  |     -7 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37018850 |                   -6 |          0 | 0.00000000000000 | No                |    37018850 |   0.023995855 | No                 |   0.000022606476 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001354616:g.37018844:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.988 | +      |  37018844 | substitution | T>A      | Intron 8  |     2961 | NM_001354616 | MLH1  | acceptor  |     -7 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37018850 |                   -6 |          0 | 0.00000000000000 | No                |    37018850 |   0.023995855 | No                 |   0.000022606476 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001354617:g.37018844:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.988 | +      |  37018844 | substitution | T>A      | Intron 9  |     2961 | NM_001354617 | MLH1  | acceptor  |     -7 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37018850 |                   -6 |          0 | 0.00000000000000 | No                |    37018850 |   0.023995855 | No                 |   0.000022606476 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001354618:g.37018844:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.988 | +      |  37018844 | substitution | T>A      | Intron 9  |     2961 | NM_001354618 | MLH1  | acceptor  |     -7 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37018850 |                   -6 |          0 | 0.00000000000000 | No                |    37018850 |   0.023995855 | No                 |   0.000022606476 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001354619:g.37018844:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.988 | +      |  37018844 | substitution | T>A      | Intron 10 |     2961 | NM_001354619 | MLH1  | acceptor  |     -7 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37018850 |                   -6 |          0 | 0.00000000000000 | No                |    37018850 |   0.023995855 | No                 |   0.000022606476 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001354620:g.37018844:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.988 | +      |  37018844 | substitution | T>A      | Intron 9  |     2961 | NM_001354620 | MLH1  | acceptor  |     -7 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37018850 |                   -6 |          0 | 0.00000000000000 | No                |    37018850 |   0.023995855 | No                 |   0.000022606476 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001354621:g.37018844:T>A  | NTR            | 00 % [00 % - 00.92 %]       |     0.000 | +      |  37018844 | substitution | T>A      | Intron 8  |     8209 | NM_001354621 | MLH1  | acceptor  |  -2810 | DeepIntron |          0 | Outside SPiCE Interpretation |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37021653 |                -2809 |   37018850 | 0.02399585516738 | No                |    37021653 |   0.241893494 | Yes                |   0.241893494461 | Yes                   |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001354622:g.37018844:T>A  | NTR            | 00 % [00 % - 00.92 %]       |     0.000 | +      |  37018844 | substitution | T>A      | Intron 9  |     5764 | NM_001354622 | MLH1  | acceptor  |  -2810 | DeepIntron |          0 | Outside SPiCE Interpretation |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37021653 |                -2809 |   37018850 | 0.02399585516738 | No                |    37021653 |   0.241893494 | Yes                |   0.241893494461 | Yes                   |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001354623:g.37018844:T>A  | NTR            | 00 % [00 % - 00.92 %]       |     0.000 | +      |  37018844 | substitution | T>A      | Intron 8  |     5764 | NM_001354623 | MLH1  | acceptor  |  -2810 | DeepIntron |          0 | Outside SPiCE Interpretation |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37021653 |                -2809 |   37018850 | 0.02399585516738 | No                |    37021653 |   0.241893494 | Yes                |   0.241893494461 | Yes                   |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001354624:g.37018844:T>A  | NTR            | 00 % [00 % - 00.92 %]       |     0.000 | +      |  37018844 | substitution | T>A      | Intron 9  |    11091 | NM_001354624 | MLH1  | donor     |   2955 | DeepIntron |          0 | Outside SPiCE Interpretation |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Don              |            37015889 |                 2956 |   37018850 | 0.02399585516738 | No                |    37026980 |   0.028353019 | No                 |   0.028353019047 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001354625:g.37018844:T>A  | NTR            | 00 % [00 % - 00.92 %]       |     0.000 | +      |  37018844 | substitution | T>A      | Intron 8  |    11091 | NM_001354625 | MLH1  | donor     |   2955 | DeepIntron |          0 | Outside SPiCE Interpretation |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Don              |            37015889 |                 2956 |   37018850 | 0.02399585516738 | No                |    37026980 |   0.028353019 | No                 |   0.028353019047 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001354626:g.37018844:T>A  | NTR            | 00 % [00 % - 00.92 %]       |     0.000 | +      |  37018844 | substitution | T>A      | Intron 9  |    11091 | NM_001354626 | MLH1  | donor     |   2955 | DeepIntron |          0 | Outside SPiCE Interpretation |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Don              |            37015889 |                 2956 |   37018850 | 0.02399585516738 | No                |    37026980 |   0.028353019 | No                 |   0.028353019047 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001354627:g.37018844:T>A  | NTR            | 00 % [00 % - 00.92 %]       |     0.000 | +      |  37018844 | substitution | T>A      | Intron 9  |    11091 | NM_001354627 | MLH1  | donor     |   2955 | DeepIntron |          0 | Outside SPiCE Interpretation |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Don              |            37015889 |                 2956 |   37018850 | 0.02399585516738 | No                |    37026980 |   0.028353019 | No                 |   0.028353019047 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001354628:g.37018844:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.988 | +      |  37018844 | substitution | T>A      | Intron 9  |     2961 | NM_001354628 | MLH1  | acceptor  |     -7 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37018850 |                   -6 |          0 | 0.00000000000000 | No                |    37018850 |   0.023995855 | No                 |   0.000022606476 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001354629:g.37018844:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.988 | +      |  37018844 | substitution | T>A      | Intron 8  |     2961 | NM_001354629 | MLH1  | acceptor  |     -7 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37018850 |                   -6 |          0 | 0.00000000000000 | No                |    37018850 |   0.023995855 | No                 |   0.000022606476 | No                    |
| chr3  |  37018844 | lol | T   | A   | .    | .      | .    | NM_001354630:g.37018844:T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.988 | +      |  37018844 | substitution | T>A      | Intron 9  |     2961 | NM_001354630 | MLH1  | acceptor  |     -7 | IntronCons |          1 | high                         |        0 |  0 | No          |            10 |    37018845 | Acc            | 0.01556491731833 | No                 | Acc              |            37018850 |                   -6 |          0 | 0.00000000000000 | No                |    37018850 |   0.023995855 | No                 |   0.000022606476 | No                    |
*** DONE Vérifier annotation SPIP sur variants confirmé
CLOSED: [2023-08-10 Thu 23:16] SCHEDULED: <2023-08-09 Wed>
**** DONE 5 variants patho tirés de l'article princips
CLOSED: [2023-08-10 Thu 23:00]
On trié par SQUIRLS décroissant
#+begin_src sh
varID
NM_000051:c.2251-10T>G
NM_000267:c.889-12T>A
NM_000059:c.8488-9T>G
NM_000249:c.589-10T>A
NM_000249:c.791-7T>A
#+end_src
***** DONE En hg38
CLOSED: [2023-08-09 Wed 22:01]
#+begin_src
spip --input test-spip.txt --output test-spip.out --GenomeAssenbly hg38 --threads 1 --maxLines 1000
#+end_src
#+RESULTS:
| varID                  | Interpretation | InterConfident              | SPiPscore | strand |    gNomen | varType      | ntChange | ExonInfo  | exonSize | transcript | gene  | NearestSS | DistSS | RegType    | SPiCEproba | SPiCEinter_2thr | deltaMES | BP  | mutInPBarea | deltaESRscore | posCryptMut | sstypeCryptMut | probaCryptMut | classProbaCryptMut | nearestSStoCrypt | nearestPosSStoCrypt | nearestDistSStoCrypt | posCryptWT | probaCryptWT | classProbaCryptWT | posSSPhysio | probaSSPhysio | classProbaSSPhysio | probaSSPhysioMut | classProbaSSPhysioMut |
| NM_000051:c.2251-10T>G | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.986 | +      | 108257471 | substitution | T>G      | Intron 14 |     1140 | NM_000051  | ATM   | acceptor  |    -10 | IntronCons |          1 | high            |        0 | 0No |          10 |     108257471 | Acc         |    0.024836003 | No            | Acc                |        108257480 |                 -10 |                    0 |          0 | No           |         108257480 | 0.006489079 | No            |     0.000004368542 | No               |                       |
| NM_000267:c.889-12T>A  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     1.000 | +      |  31200410 | substitution | T>A      | Intron 8  |    17756 | NM_000267  | NF1   | acceptor  |    -12 | IntronCons |          1 | high            |        0 | 0No |          10 |      31200411 | Acc         |    0.009082899 | No            | Acc                |         31200421 |                 -11 |                    0 |          0 | No           |          31200421 | 0.005160854 | No            |     0.000003718518 | No               |                       |
| NM_000059:c.8488-9T>G  | Alter by SPiCE | 98.41 % [91.47 % - 99.96 %] |     0.994 | +      |  32370947 | substitution | T>G      | Intron 19 |      398 | NM_000059  | BRCA2 | acceptor  |