apraga/org - Change L57R65QXZBKUKBRT7T5Z74JRZPOWTJZY4F7OEDBK24Q2BFVA3INQC

dbSNP common not clinvar patho: ne pas utiliser dbSNP

Created by Alexis Praga on December 4, 2022

L57R65QXZBKUKBRT7T5Z74JRZPOWTJZY4F7OEDBK24Q2BFVA3INQC

Dependencies

In channels

main

Change contents

Insertion in workout.org at line 5645 [5.1]

[4.131]

* <2022-12-03 Sat> Press handstand
- Pancake split 5x3 (coin du lit)
- Legs raise 5x3

Replacement in projects.org at line 1620 [5.123895]
∅:D[6.1662] → [7.74:88]
B:BD[7.74] → [7.74:88]
```
- [ ] VEP 20G
```
[6.1662]
[8.299]
```
- [X] VEP 20G
- [X] transcriptome (spip)
```

Replacement in projects.org at line 1664 [5.123895]

B:BD[9.1275] → [10.12:63]

******* TODO classification clinvar codée dbSNP ?

[9.1275]

[10.63]

******* KILL classification clinvar codée dbSNP ?
CLOSED: [2022-12-04 Sun 14:38]

Insertion in projects.org at line 1673 [5.123895]
[10.433]
[10.433]
```
Il faut également les likely patho et conflicting
```

Replacement in projects.org at line 1675 [5.123895]

B:BD[10.478] → [10.478:633]

bncftools query -f '%INFO/CLNSIG\n' dbSNP_common_chr20.vcf.gz -i
'INFO/CLNSIG[*]~"^5|" | INFO/CLNSIG[*]=="5" | INFO/CLNSIG[*]~"|5"'| sort | uniq
#+end_src

[10.478]

[10.633]

bcftools query -f '%INFO/CLNSIG\n' dbSNP_common_chr20.vcf.gz -i \
'INFO/CLNSIG[*]~"^5|" | INFO/CLNSIG[*]=="5" | INFO/CLNSIG[*]~"|5" | INFO/CLNSIG[*]~"^4|" | INFO/CLNSIG[*]=="4" | INFO/CLNSIG[*]~"|4" | INFO/CLNSIG[*]~"^12|" | INFO/CLNSIG[*]=="12" | INFO/CLNSIG[*]~"|12"' | sort

Deletion in projects.org at line 1678 [5.123895]

B:BD[10.634] → [10.634:971]

B:BD[10.971] → [11.493:649]

∅:D[11.649] → [10.1127:1172]

B:BD[10.1127] → [10.1127:1172]

B:BD[10.1172] → [11.650:712]

Si on exclut tous les patho:
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools query -f '%ID\n' dbSNP_common_chr20.vcf.gz -e 'INFO/CLNSIG[*]~"^5|" | INFO/CLNSIG[*]=="5" | INFO/CLNSIG[*]~"|5"'| sort | uniq | wc -l
#+end_src
#+RESULTS:
: 518842
On en a 10 de plus que la version d'Alexis
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools query -f '%ID\n' dbSNP_common_chr20.vcf.gz -e 'INFO/CLNSIG[*]=="5" | INFO/CLNSIG[*]~"^5|" | INFO/CLNSIG[*]~"|5"' | sort > common-notpatho-test.txt
sort common-notpatho-alexis.txt > sorted.txt
comm -23 common-notpatho-test.txt sorted.txt > missing_id.txt

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| . |  . | 12 |    |   |   |   |   |   |   |   |
| . | 12 |  0 |  2 |   |   |   |   |   |   |   |
| 2 |  3 |  2 |  2 | 2 | 5 | . |   |   |   |   |
| . |  2 |  3 |  2 | 2 | 4 |   |   |   |   |   |
| . |  . |  3 | 12 | 3 |   |   |   |   |   |   |
| . |  5 |  2 |  . |   |   |   |   |   |   |   |
| . |  . |  . |  5 | 2 | 2 |   |   |   |   |   |
| . |  9 |  9 |  9 | 5 | 5 | 2 | 3 | 2 | 3 | 2 |

Deletion in projects.org at line 1690 [5.123895]

B:BD[11.714] → [12.738:1141]

On génère les positions à chercher dans clinvar.NB: je ne comprends pas pourquoi les régions ne fonctionne pas bien...  On fait juste un grep
#+begin_src sh :dir ~/code/bisonex/test_isec
# bcftools query -f '%CHROM\t%POS\t%POS\n' -i 'ID=@missing_id.txt' dbSNP_common_chr20.vcf.gz > to_search.txt
bcftools query -f '%POS\n' -i 'ID=@missing_id.txt' dbSNP_common_chr20.vcf.gz > to_search.txt
#+end_src

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```
#+RESULTS:
Puis on regarde à la main les variations...
```
[12.1142]
[12.1199]
```
Si on les exclut :
```

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B:BD[12.1244] → [12.1244:1457]

bcftools query -f '%POS %REF %ALT\ %INFO/CLNSIG\n' -i 'ID=@missing_id.txt' dbSNP_common_chr20.vcf.gz
bcftools query -f '%POS %REF %ALT %INFO/CLNSIG\n'  clinvar_chr20.vcf.gz | zgrep -f to_search.txt > to_check.txt

[12.1244]

[12.1457]

bcftools query -f '%ID\n' dbSNP_common_chr20.vcf.gz -e \
'INFO/CLNSIG[*]~"^5|" | INFO/CLNSIG[*]=="5" | INFO/CLNSIG[*]~"|5" | INFO/CLNSIG[*]~"4" | INFO/CLNSIG[*]~"12"' | sort | uniq > common-notpatho.txt

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B:BD[12.1479] → [12.1479:2247]

| 3234173 T A    | C   | G . | . | . |  2 | 2 |   |   |   |   |
| 10658574 G A   | T . |   2 | 3 | 2 |  2 | 4 |   |   |   |   |
| 10672794 G A   | C . |   2 | 3 | 2 |  2 | 0 | 0 |   |   |   |
| 18525868 C T . | 0   |   2 |   |   |    |   |   |   |   |   |
| 25390747 G C . | 0   |     |   |   |    |   |   |   |   |   |
| 32800145 C G   | T . |   2 | 2 | 3 |  0 | 2 |   |   |   |   |
| 33412656 C G   | T . |   . | 2 | 2 |  0 | 2 |   |   |   |   |
| 45891622 G A   | C   | T . | . | 3 | 12 | 3 |   |   |   |   |
| 54171651 G A   | T . |  12 | 0 | 2 |    |   |   |   |   |   |
| 62172726 G A . | 0   |     |   |   |    |   |   |   |   |   |
| 63349782 G A   | C . |  11 | 2 | 2 |  2 | 0 |   |   |   |   |
| 63414925 G A   | C   | T . | 3 | 0 |  3 | 2 | 2 | 2 | 2 | . |

Replacement in projects.org at line 1699 [5.123895]

B:BD[12.2248] → [12.2248:2285]

∅:D[12.2285] → [13.12:104]

B:BD[11.900] → [13.12:104]

ON ne retrouve que des conflicting !
******* Corriger script alexi
Version initiale
#+begin_src sh :dir ~/code/bisonex/test_isec

[12.2248]

[13.104]

 #+begin_src sh :dir ~/code/bisonex/test_isec

Replacement in projects.org at line 1706 [5.123895]
B:BD[13.363] → [13.363:405]
```
sort tmp.txt > common-notpatho-alexis.txt
```
[13.363]
[13.405]
```
sort tmp.txt | uniq > common-notpatho-alexis.txt
```
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```
#+end_src
```
[13.438]
[10.1431]
```
 #+end_src
```
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B:BD[10.1432] → [13.449:496]
```
#+RESULTS:
: 518832 common-notpatho-alexis.txt
```
[10.1432]
[13.496]
```
 #+RESULTS:
 : 518832 common-notpatho-alexis.txt
```

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B:BD[13.497] → [13.497:523]

En changeant la condition

[13.497]

[13.523]

On en a 6 de plus que la version d'Alexis mais quelques différences
Ceux d'Alexis qui manquent:

Replacement in projects.org at line 1717 [5.123895]

B:BD[13.568] → [13.568:1087]

sed  's/if '\''PATHO'\'' in clinvarline\[7\].upper():/if "Pathogenic" in clinvarline[7]:/' ../script/pythonScript/clinvar_sbSNP.py > ../script/pythonScript/clinvar_sbSNP_patch.py
snp=dbSNP_common_chr20.vcf.gz
clinvar=clinvar_chr20_notremapped.vcf.gz
python ../script/pythonScript/clinvar_sbSNP_patch.py \
    --clinvar $clinvar \
    --chrm_name_table ../database/RefSeq/refseq_to_number_only_consensual.txt \
    --dbSNP $snp --output tmp.txt
sort tmp.txt > common-notpatho-alexis.txt
wc -l common-notpatho-alexis.txt

[13.568]

[13.1087]

comm -23 common-notpatho-alexis.txt common-notpatho.txt > alexis-only.txt
cat alexis-only.txt

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B:BD[13.1109] → [13.1109:1186]

: 518844 common-notpatho-alexis.txt
Maitenat, 2 de plus que notre version...

[13.1109]

[13.1186]

| rs1064039  |
| rs3833341  |
| rs73598374 |

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[13.1187]
[13.1187]
```
On les teste dans clinvar et dbSNP
```

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B:BD[13.1232] → [13.1232:1322]

sort common-notpatho-alexis.txt > sorted.txt
comm -23 sorted.txt common-notpatho-test.txt

[13.1232]

[13.1322]

bcftools query -f '%POS %REF %ALT %INFO/CLNSIG\n' -i 'ID=@alexis-only.txt' dbSNP_common_chr20.vcf.gz
bcftools query -f '%POS\n' -i 'ID=@alexis-only.txt' dbSNP_common_chr20.vcf.gz > alexis-only-pos.txt
while read  -r line; do
bcftools query -f '%POS %REF %ALT %INFO/CLNSIG\n' -i 'POS='$line clinvar_chr20.vcf.gz
done < alexis-only-pos.txt
# bcftools query -f '%POS %REF %ALT %INFO/CLNSIG\n' -i 'POS=23637790' clinvar_chr20.vcf.gz

Replacement in projects.org at line 1737 [5.123895]

B:BD[13.1344] → [13.1344:1374]

| rs3833341  |
| rs73598374 |

[13.1344]

[13.1374]

|   764018 | A | ACAGGTCAAT,ACAGGT | .,5     | 2,. |   |
| 23637790 | C | G,T               | .,.,12  |     |   |
| 44651586 | C | A,G,T             | .,.,.,5 |   2 | 2 |
|   764018 | A | ACAGGTCAAT        | Benign  |     |   |
| 23637790 | C | T                 | Benign  |     |   |
| 44651586 | C | T                 | Benign  |     |   |
On a donc une discordance entre clinvar et dbSNP.
On dirait qu'ils ont mal fait l'intersection avec clinvar.
Par exemple https://www.ncbi.nlm.nih.gov/snp/rs3833341#clinical_significance
Tu as l'impression qu'il y a un 1 clinvar bénin et 1 patho.

Replacement in projects.org at line 1751 [5.123895]

B:BD[13.1375] → [13.1375:1406]

rs1799990
rs3833341
rs73598374

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[13.1406]

En cherchant par NM, tu vois qu'il est bénin sur clinvar car il y a d'autres soumissions ! https://www.ncbi.nlm.nih.gov/clinvar/variation/262235/
Confirmation sur nos bases de données :
$ bcftools query -f '%POS %REF %ALT %INFO/CLNSIG\n' -i 'POS=764018' dbSNP_common_chr20.vcf.gz
764018 A ACAGGTCAAT,ACAGGT .,5|2,.
$ bcftools query -f '%POS %REF %ALT %INFO/CLNSIG\n' -i 'POS=764018' clinvar_chr20.vcf.gz
764018 A ACAGGTCAAT Benign

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******* KILL Corriger script alexi
CLOSED: [2022-12-04 Sun 13:03]
Gère clinvar patho, probablement patho ou conflicting !

Insertion in projects.org at line 2198 [5.123895]
[14.113]
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```
Contribuer pull request
```
Replacement in projects.org at line 2203 [5.123895]
B:BD[14.185] → [9.5332:5354]
∅:D[9.5354] → [16.1559:1590]
B:BD[16.1559] → [16.1559:1590]
```
***** KILL 'rtg-tools
CLOSED: [2022-11-19 Sat 21:06]
```
[14.185]
[17.5199]
```
Contribuer pull request
***** HOLD rtg-tools
```
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B:BD[17.5220] → [14.229:245]
```
***** TODO Spip
```
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```
***** DONE Spip
CLOSED: [2022-12-04 Sun 12:49]
Pas de pull request
```
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∅:D[18.587] → [19.524:541]
∅:D[16.2612] → [19.524:541]
B:BD[20.734] → [19.524:541]
```
**** TODO Divers
```
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```
**** Divers
```

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∅:D[6.1999] → [22.451:467]

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**** TODO Sarek

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**** TODO Genome in a bottle ?
On n'a pas l'ADN.. séquencer à Centogène ?
*** Améliorations
**** TODO Utilise une versionn allégée de GnomAD (une seule colonne)
**** TODO Utiliser T-to-T comme références
**** TODO Digenisme (cf nomenclature omim)
C’est dans le nom de la maladie
**** TODO Macro excel
*** HOLD Implémenter d’autres pipeline
Voir https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04407-x
**** KILL GATK
CLOSED: [2022   -11-11 Fri 20:01]
https://broadinstitute.github.io/warp/docs/Pipelines/Exome_Germline_Single_Sample_Pipeline/README
A priori, respecte les bonnes pratiques
**** KILL Essayer snmake avec bonne pratiques
https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling/blob/main/.github/workflows/main.yml
Installer Mamba (micromamba ne fonctionne pas sous nix)
Ne fonctionne pas sous WSL2... MultiQC n’est pas assez à jour
Problèmes de versions...
**** HOLD Sarek

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∅:D[2.1331] → [22.565:649]

B:BD[22.565] → [22.565:649]

***** TODO Dérivation nix pour modules python
***** TODO Lancer sarek en mode test

[2.1331]

[22.649]

***** HOLD Dérivation nix pour modules python
***** HOLD Lancer sarek en mode test

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B:BD[22.814] → [22.814:862]

B:BD[23.2077] → [22.863:896]

B:BD[24.87] → [25.1589:1635]

B:BD[25.1635] → [18.588:822]

∅:D[20.764] → [26.15:57]

∅:D[18.822] → [26.15:57]

∅:D[23.2134] → [26.15:57]

B:BD[27.1499] → [26.15:57]

∅:D[26.57] → [27.1500:1585]

B:BD[28.182] → [27.1500:1585]

B:BD[27.1585] → [18.823:872]

∅:D[26.73] → [24.216:314]

∅:D[28.192] → [24.216:314]

∅:D[18.872] → [24.216:314]

B:BD[24.216] → [24.216:314]

B:BD[24.314] → [26.74:114]

B:BD[26.114] → [18.873:919]

∅:D[29.912] → [26.160:412]

∅:D[18.919] → [26.160:412]

B:BD[26.160] → [26.160:412]

B:BD[26.412] → [29.913:960]

***** TODO Lancer sarek sur données allégées
**** TODO Genome in a bottle ?
On n'a pas l'ADN.. séquencer à Centogène ?
*** Améliorations
**** TODO Utilise une versionn allégée de GnomAD (une seule colonne)
**** TODO Utiliser T-to-T comme références
**** TODO Digenisme (cf nomenclature omim)
C’est dans le nom de la maladie
**** TODO Macro excel
*** TODO Implémenter d’autres pipeline
Voir https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04407-x
**** KILL GATK
CLOSED: [2022   -11-11 Fri 20:01]
https://broadinstitute.github.io/warp/docs/Pipelines/Exome_Germline_Single_Sample_Pipeline/README
A priori, respecte les bonnes pratiques
**** KILL Essayer snmake avec bonne pratiques
https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling/blob/main/.github/workflows/main.yml
Installer Mamba (micromamba ne fonctionne pas sous nix)
Ne fonctionne pas sous WSL2... MultiQC n’est pas assez à jour
Problèmes de versions...
**** TODO Les pipeline de nf-core:
***** Sarek

[22.814]

[30.11224]

***** HOLD Lancer sarek sur données allégées

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```
Essayer dernière version de kent
```
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∅:D[31.445] → [34.81:82]
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∅:D[34.113] → [32.140:168]
B:BD[32.140] → [32.140:168]
```
** WAIT Nixpkg for BioExtAlign
SCHEDULED: <2022-08-10 Wed>
```
[33.134]
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```
** DONE Nixpkg for BioExtAlign
CLOSED: [2022-10-22 Sat 12:43] SCHEDULED: <2022-08-10 Wed>
```

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B:BD[23.2398] → [3.1414:1453]

SCHEDULED: <2022-11-14 Mon>
À partir de début décement novembre

[23.2370]

[17.5260]

SCHEDULED: <2022-12-05 Mon>
"Je veux changer d'abonnement sur la hotline" pour avoir le service commercial

dbSNP common not clinvar patho: ne pas utiliser dbSNP

Dependencies

In channels

Change contents

Insertion in workout.org at line 5645 [5.1]

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