apraga/org - Change 7ZYARVJDIHXIVMIINQT7CLFHTTNJ5AZ3OZ7KWOL3QTOOXZSY74BAC

Bisonex save

Created by Alexis Praga on April 18, 2023

7ZYARVJDIHXIVMIINQT7CLFHTTNJ5AZ3OZ7KWOL3QTOOXZSY74BAC

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main

Change contents

Insertion in projects.org at line 2145 [5.123895]

[3.1300]

[4.316]

** TODO Don index nzb
SCHEDULED: <2023-04-19 Wed>
/Entered on/ [2023-04-16 Sun 16:53]

Replacement in projects/bisonex.org at line 38 [6.35]

B:BD[2.40971] → [2.40971:45690]

.gz -bg
#+end_src
#+begin_src  sh
NXF_OPTS=-D"user.name=${USER}" nextflow run workflows/compareVCF.nf -profile standard,helios -resume --outdir=compareHG003  --test.id=HG003 --test.query=out/HG003_1/variantCalling/haplotypecaller/HG003_1.vcf.gz  --test.compare=vcfeval,happy --test.capture=data/AgilentSureSelectv05_hg38.bed
#+end_src
vcfeval
Threshold  True-pos-baseline  True-pos-call  False-pos  False-neg  Precision  Sensitivity  F-measure
----------------------------------------------------------------------------------------------------
    5.000              36745          36473        486       3988     0.9869       0.9021     0.9426
     None              36748          36476        495       3985     0.9866       0.9022     0.9425
$ zcat NA12878.snp_roc.tsv.gz  | tail -n 1 | awk '{print $7 $6}'
happy
Type Filter  TRUTH.TOTAL  TRUTH.TP  TRUTH.FN  QUERY.TOTAL  QUERY.FP  QUERY.UNK  FP.gt  FP.al  METRIC.Recall  METRIC.Precision  METRIC.Frac_NA  METRIC.F1_Score  TRUTH.TOTAL.TiTv_ratio  QUERY.TOTAL.TiTv_ratio  TRUTH.TOTAL.het_hom_ratio  QUERY.TOTAL.het_hom_ratio
INDEL    ALL         2731      2290       441         3092       208        577     62     53       0.838521          0.917296        0.186611         0.876141                     NaN                     NaN                   1.505145                   1.888993
INDEL   PASS         2731      2290       441         3092       208        577     62     53       0.838521          0.917296        0.186611         0.876141                     NaN                     NaN                   1.505145                   1.888993
  SNP    ALL        37997     34481      3516        36861       306       2074     33     13       0.907466          0.991204        0.056265         0.947488                2.611269                2.565915                   1.555780                   1.621727
  SNP   PASS        37997     34481      3516        36861       306       2074     33     13       0.907466          0.991204        0.056265         0.947488                2.611269                2.5659
**** DONE HG004
CLOSED: [2023-04-16 Sun 00:20]
#+begin_src sh
NXF_OPTS=-D"user.name=${USER}" nextflow run main.nf -profile standard,helios  --input /Work/Groups/bisonex/data/giab/GRCh38/HG004_{1,2}.fq.gz -bg
#+end_src
vcfeval
Threshold  True-pos-baseline  True-pos-call  False-pos  False-neg  Precision  Sensitivity  F-measure
----------------------------------------------------------------------------------------------------
    6.000              36938          36678        421       4040     0.9887       0.9014     0.9430
     None              36942          36682        432       4036     0.9884       0.9015     0.9429
happy
 Type Filter  TRUTH.TOTAL  TRUTH.TP  TRUTH.FN  QUERY.TOTAL  QUERY.FP  QUERY.UNK  FP.gt  FP.al  METRIC.Recall  METRIC.Precision  METRIC.Frac_NA  METRIC.F1_Score  TRUTH.TOTAL.TiTv_ratio  QUERY.TOTAL.TiTv_ratio  TRUTH.TOTAL.het_hom_ratio  QUERY.TOTAL.het_hom_ratio
INDEL    ALL         2787      2388       399         3183       195        580     53     38       0.856835          0.925086        0.182218         0.889654                     NaN                     NaN                   1.507834                   1.848649
INDEL   PASS         2787      2388       399         3183       195        580     53     38       0.856835          0.925086        0.182218         0.889654                     NaN                     NaN                   1.507834                   1.848649
  SNP    ALL        38185     34560      3625        36921       254       2107     46      7       0.905067          0.992704        0.057068         0.946862                2.589175                2.553546                   1.632595                   1.653534
  SNP   PASS        38185     34560      3625        36921       254       2107     46      7       0.905067          0.992704        0.057068         0.946862                2.589175                2.553546                   1.632595                   1.653534
**** DONE Résumer résultats pour Paul + article :resultats:
CLOSED: [2023-04-06 Thu 21:41] SCHEDULED: <2023-04-02 Sun>
*** TODO Platinum genome
https://emea.illumina.com/platinumgenomes.html
*** TODO Séquencer NA12878
Discussion avec Paul : sous-traitant ne nous donnera pas les données, il faut commander l'ADN
** TODO Fastq avec tous les variants centogène
*** TODO Extraire liste des variants
SCHEDULED: <2023-04-17 Mon>
*** TODO Générer fastq
SCHEDULED: <2023-04-16 Sun>
*** TODO Vérifier qu'on les retrouve tous
SCHEDULED: <2023-04-17 Mon>
** Divers
*** DONE Vérifier nombre de reads fastq - bam
CLOSED: [2022-10-09 Sun 22:31]

[2.40971]

.gz -bg
#+end_src
#+begin_src  sh
NXF_OPTS=-D"user.name=${USER}" nextflow run workflows/compareVCF.nf -profile standard,helios -resume --outdir=compareHG003  --test.id=HG003 --test.query=out/HG003_1/variantCalling/haplotypecaller/HG003_1.vcf.gz  --test.compare=vcfeval,happy --test.capture=data/AgilentSureSelectv05_hg38.bed
#+end_src
vcfeval
Threshold  True-pos-baseline  True-pos-call  False-pos  False-neg  Precision  Sensitivity  F-measure
----------------------------------------------------------------------------------------------------
    5.000              36745          36473        486       3988     0.9869       0.9021     0.9426
     None              36748          36476        495       3985     0.9866       0.9022     0.9425
$ zcat NA12878.snp_roc.tsv.gz  | tail -n 1 | awk '{print $7 $6}'
happy
Type Filter  TRUTH.TOTAL  TRUTH.TP  TRUTH.FN  QUERY.TOTAL  QUERY.FP  QUERY.UNK  FP.gt  FP.al  METRIC.Recall  METRIC.Precision  METRIC.Frac_NA  METRIC.F1_Score  TRUTH.TOTAL.TiTv_ratio  QUERY.TOTAL.TiTv_ratio  TRUTH.TOTAL.het_hom_ratio  QUERY.TOTAL.het_hom_ratio
INDEL    ALL         2731      2290       441         3092       208        577     62     53       0.838521          0.917296        0.186611         0.876141                     NaN                     NaN                   1.505145                   1.888993
INDEL   PASS         2731      2290       441         3092       208        577     62     53       0.838521          0.917296        0.186611         0.876141                     NaN                     NaN                   1.505145                   1.888993
  SNP    ALL        37997     34481      3516        36861       306       2074     33     13       0.907466          0.991204        0.056265         0.947488                2.611269                2.565915                   1.555780                   1.621727
  SNP   PASS        37997     34481      3516        36861       306       2074     33     13       0.907466          0.991204        0.056265         0.947488                2.611269                2.5659
**** DONE HG004
CLOSED: [2023-04-16 Sun 00:20]
#+begin_src sh
NXF_OPTS=-D"user.name=${USER}" nextflow run main.nf -profile standard,helios  --input /Work/Groups/bisonex/data/giab/GRCh38/HG004_{1,2}.fq.gz -bg
#+end_src
vcfeval
Threshold  True-pos-baseline  True-pos-call  False-pos  False-neg  Precision  Sensitivity  F-measure
----------------------------------------------------------------------------------------------------
    6.000              36938          36678        421       4040     0.9887       0.9014     0.9430
     None              36942          36682        432       4036     0.9884       0.9015     0.9429
happy
 Type Filter  TRUTH.TOTAL  TRUTH.TP  TRUTH.FN  QUERY.TOTAL  QUERY.FP  QUERY.UNK  FP.gt  FP.al  METRIC.Recall  METRIC.Precision  METRIC.Frac_NA  METRIC.F1_Score  TRUTH.TOTAL.TiTv_ratio  QUERY.TOTAL.TiTv_ratio  TRUTH.TOTAL.het_hom_ratio  QUERY.TOTAL.het_hom_ratio
INDEL    ALL         2787      2388       399         3183       195        580     53     38       0.856835          0.925086        0.182218         0.889654                     NaN                     NaN                   1.507834                   1.848649
INDEL   PASS         2787      2388       399         3183       195        580     53     38       0.856835          0.925086        0.182218         0.889654                     NaN                     NaN                   1.507834                   1.848649
  SNP    ALL        38185     34560      3625        36921       254       2107     46      7       0.905067          0.992704        0.057068         0.946862                2.589175                2.553546                   1.632595                   1.653534
  SNP   PASS        38185     34560      3625        36921       254       2107     46      7       0.905067          0.992704        0.057068         0.946862                2.589175                2.553546                   1.632595                   1.653534
**** DONE Résumer résultats pour Paul + article :resultats:
CLOSED: [2023-04-06 Thu 21:41] SCHEDULED: <2023-04-02 Sun>
**** DONE Plot : ashkenazim trio
CLOSED: [2023-04-18 Tue 21:27] SCHEDULED: <2023-04-16 Sun>
/Entered on/ [2023-04-16 Sun 17:29]
*** TODO Platinum genome
https://emea.illumina.com/platinumgenomes.html
*** TODO Séquencer NA12878
Discussion avec Paul : sous-traitant ne nous donnera pas les données, il faut commander l'ADN
** TODO Fastq avec tous les variants centogène
*** TODO Extraire liste des variants
SCHEDULED: <2023-04-17 Mon>
*** TODO Générer fastq
SCHEDULED: <2023-04-16 Sun>
*** TODO Vérifier qu'on les retrouve tous
SCHEDULED: <2023-04-17 Mon>
** Divers
*** DONE Vérifier nombre de reads fastq - bam
CLOSED: [2022-10-09 Sun 22:31]
* TODO Plot : ashkenazim trio
SCHEDULED: <2023-04-16 Sun>
/Entered on/ [2023-04-16 Sun 17:29]