* <2023-08-08 Tue> Tricking
kick 25x2
roundhouse kick x2 each side x25
cartwheel x15

** TODO Copie carte d'identié + mutuelle accueil hôpital
SCHEDULED: <2023-08-10 Thu>
/Entered on/ [2023-08-08 Tue 21:18]

*** 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
*** PROJ [#A] Porter Spip
*** TODO Générer la base de donnée spip
SCHEDULED: <2023-08-03 Thu 11:30>
**** PROJ Vérifier la génération du transcriptome en hg38: checksum différent
- [X] Nettoyer et vérifier sur hg38 avec ediff les RData : différent
- [X] Sinon, ne pas nettoyer et générer: idem
**** TODO Récupérer ncbi RefSeq curated
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
Avec "*", les champs conservés (a priori)
|  1 | bin          | Indexing field to speed chromosome range queries.                       |
|  2 | *name        | Name of gene (usually transcript_id from GTF)                           |
|  3 | *chrom       | Reference sequence chromosome or scaffold                               |
|  4 | *strand      | + or - for strand                                                       |
|  5 | *txStart     | Transcription start position (or end position for minus strand item)    |
|  6 | *txEnd       | Transcription end position (or start position for minus strand item)    |
|  7 | *cdsStart    | Coding region start (or end position for minus strand item)             |
|  8 | *cdsEnd      | Coding region end (or start position for minus strand item)             |
|  9 | *exonCount   | Number of exons                                                         |
| 10 | *exonStarts  | Exon start positions (or end positions for minus strand item)           |
| 11 | *exonEnds    | Exon end positions (or start positions for minus strand item)           |
| 12 | *score       | score                                                                   |
| 13 | *name2       | Alternate name (e.g. gene_id from GTF)                                  |
| 14 | cdsStartStat | Status of CDS start annotation (none, unknown, incomplete, or complete) |
| 15 | cdsEndStat   | Status of CDS end annotation (none, unknown, incomplete, or complete)   |
| 16 | exonFrames   | Exon frame {0,1,2}, or -1 if no frame for exon                          |
ex:
585     NR_046018.2     chr1    +       11873   14409   14409   14409   3       11873,12612,13220,      12227,12721,14409,      0       DDX11L1 none    none    -1,-1,-1,
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:
 1 #chrom
 2 chromStart
 3 chromEnd
 4 name
 5 score
 6  strand
 7 thickStart
 8 thickEnd
 9 reserved
10 blockCount
11 blockSizes
12 chromStarts
13 name2
14 cdsStartStat
15 cdsEndStat
16 exonFrames
17 type
18 geneName
19 geneName2
20 geneType
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
*** TODO Tester correspondance partielle ?
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
*** PROJ [#A] Filtre vep (avec spip ?)
** PROJ [#B] Indicateurs qualité
*** Idée
Raredisease:
- FastQC : nombreuses statistiques. Non disponible Nix
- Mosdepth : calcule la profondeur (2x plus rapide que samtools depth). Nix
- MultiQC : fusionne juste les résultats des analyses. Non disponible nix
- Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics
- Qualimap : alternative fastqc ? Non disponible nix
- Sentieon's WgsMetricsAlgo : propriétaire
- TIDDIT's cov : TIDIT = remaninement chromosomique
Sarek:
- alignment statistics : samtools stats, mosdepth
- QC : MultiQC
MultiQC : non disponible Nix
** PROJ [#B] Compte-redu exécution avec MultiQC
** PROJ vérifier si normalisation
** PROJ [#B] Vérification nomenclature hgvs avec mutalyzer
** DONE Exécution
CLOSED: [2022-09-13 Tue 21:37]
*** KILL test Bionix
*** KILL Implémenter execution avec Nix ?
Voir https://academic.oup.com/gigascience/article/9/11/giaa121/5987272?login=false
pour un exemple.
Probablement plus simple d’utiliser Nix pour gestion de l’environnement et snakemake pour l’exécution
Pas d’accès internet depuis le cluster
*** DONE nextflow
CLOSED: [2022-09-13 Tue 21:37]
**** TODO Bug scheduler SGE
Le job se fait tuer car l'utilisateur n'est pas passé correctement à nextflow
***** DONE Forcer l'utilisateur à l'exécution
CLOSED: [2023-04-01 Sat 17:57]
NXF_OPTS=-D"user.name=alex"
***** DONE Vérifier si le problème persiste avec 22.10.6
CLOSED: [2023-04-01 Sat 18:38] SCHEDULED: <2023-04-01 Sat>
oui
***** KILL Packager l'utilisateur dans le programme ?
Mauvaise idée..
** TODO Preprocessing avec nextflow
*** TODO Map to reference
**** TODO Sample ID dans header
/Work/Users/apraga/bisonex/out/63003856_S135/preprocessing/baserecalibrator
*** DONE Mark duplicate
CLOSED: [2022-10-09 Sun 22:30]
*** DONE Recalibrate base quality score
CLOSED: [2022-10-09 Sun 22:30]
** DONE Variant calling avec Nextflow
CLOSED: [2022-11-19 Sat 21:34]
*** DONE Haplotype caller
CLOSED: [2022-10-09 Sun 22:40]
*** DONE Filter variants
CLOSED: [2022-10-09 Sun 22:40]
*** DONE Filter common snp not clinvar path
CLOSED: [2022-11-07 Mon 23:00]
Voir [[*common dbSNP not clinvar patho][common dbSNP not clinvar patho]]
*** DONE Filter variant only in consensual sequence
CLOSED: [2022-11-08 Tue 22:23]
*** DONE Filter technical variants
CLOSED: [2022-11-19 Sat 21:34]
*** DONE Utilise AVX pour accélerer l'exécution
CLOSED: [2023-04-29 Sat 15:46]
Sans cela, on a l'avertissement
#+begin_quote
17:28:00.720 INFO  PairHMM - OpenMP multi-threaded AVX-accelerated native PairHMM implementation is not supported
17:28:00.721 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/nix/store/cy9ckxqwrkifx7wf02hm4ww1p6lnbxg9-gatk-4.2.4.1/bin/gatk-package-4.2.4.1-local.jar!/com/intel/gkl/native/libgkl_utils.so
17:28:00.733 WARN  NativeLibraryLoader - Unable to load libgkl_utils.so from native/libgkl_utils.so (/Work/Users/apraga/bisonex/out/NA12878_NIST7035/preprocessing/applybqsr/libgkl_utils821485189051585397.so: libgomp.so.1: cannot open shared object file: No such file or directory)
17:28:00.733 WARN  IntelPairHmm - Intel GKL Utils not loaded
17:28:00.733 WARN  PairHMM - ***WARNING: Machine does not have the AVX instruction set support needed for the accelerated AVX PairHmm. Falling back to the MUCH slower LOGLESS_CACHING implementation!
17:28:00.763 INFO  ProgressMeter - Starting traversal
#+end_quote
libgomp.so est fourni par gcc donc il faut charger le module
 module load gcc@11.3.0/gcc-12.1.0
** KILL Utiliser subworkflow
CLOSED: [2023-04-02 Sun 18:08]
Notre version permet d'être plus souple

*** 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
*** PROJ [#A] Porter Spip
*** DONE Générer la base de donnée 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 Vérifier annotation SPIP sur variants confirmer
SCHEDULED: <2023-08-09 Wed>
**** 5 variants patho tirés de l'article princips
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  |     -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               |                       |
Test sur mobidetails : 98% pour spip (! différent du fichier excel...)
Second variant: ok en VCf également
***** DONE Lifter les variants T2T : ok ! mais multiples trnascrits en génomique ...
CLOSED: [2023-08-09 Wed 23:23] SCHEDULED: <2023-08-09 Wed>
##fileformat=VCFv4.0
##assembly=GRCh38/hg38
##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	.	.	.
❯ ./result/bin/spip -I test-spip-T2T.vcf -O test-spip-T2T.out -g hs1 --refseq dataRefSeqhs1.RData --transcriptome transcriptome_hs1.RData
        #+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                    |
|       |           |     |     |     |      |        |      |                              |                |                             |           |        |           |              |          |           |          |              |       |           |        |            |            |                              |          |    |             |               |             |                |                  |                    |                  |                     |                      |            |                  |                   |             |               |                    |                  |                       |
***** TODO Comment gérer les multiples transcripts ?
SCHEDULED: <2023-08-09 Wed>
*** PROJ [#A] Filtre vep (avec spip ?)
** PROJ [#B] Indicateurs qualité
*** Idée
Raredisease:
- FastQC : nombreuses statistiques. Non disponible Nix
- Mosdepth : calcule la profondeur (2x plus rapide que samtools depth). Nix
- MultiQC : fusionne juste les résultats des analyses. Non disponible nix
- Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics
- Qualimap : alternative fastqc ? Non disponible nix
- Sentieon's WgsMetricsAlgo : propriétaire
- TIDDIT's cov : TIDIT = remaninement chromosomique
Sarek:
- alignment statistics : samtools stats, mosdepth
- QC : MultiQC
MultiQC : non disponible Nix
** PROJ [#B] Compte-redu exécution avec MultiQC
** PROJ vérifier si normalisation
** PROJ [#B] Vérification nomenclature hgvs avec mutalyzer
** DONE Exécution
CLOSED: [2022-09-13 Tue 21:37]
*** KILL test Bionix
*** KILL Implémenter execution avec Nix ?
Voir https://academic.oup.com/gigascience/article/9/11/giaa121/5987272?login=false
pour un exemple.
Probablement plus simple d’utiliser Nix pour gestion de l’environnement et snakemake pour l’exécution
Pas d’accès internet depuis le cluster
*** DONE nextflow
CLOSED: [2022-09-13 Tue 21:37]
**** TODO Bug scheduler SGE
Le job se fait tuer car l'utilisateur n'est pas passé correctement à nextflow
***** DONE Forcer l'utilisateur à l'exécution
CLOSED: [2023-04-01 Sat 17:57]
NXF_OPTS=-D"user.name=alex"
***** DONE Vérifier si le problème persiste avec 22.10.6
CLOSED: [2023-04-01 Sat 18:38] SCHEDULED: <2023-04-01 Sat>
oui
***** KILL Packager l'utilisateur dans le programme ?
Mauvaise idée..
** TODO Preprocessing avec nextflow
*** TODO Map to reference
**** TODO Sample ID dans header
/Work/Users/apraga/bisonex/out/63003856_S135/preprocessing/baserecalibrator
*** DONE Mark duplicate
CLOSED: [2022-10-09 Sun 22:30]
*** DONE Recalibrate base quality score
CLOSED: [2022-10-09 Sun 22:30]
** DONE Variant calling avec Nextflow
CLOSED: [2022-11-19 Sat 21:34]
*** DONE Haplotype caller
CLOSED: [2022-10-09 Sun 22:40]
*** DONE Filter variants
CLOSED: [2022-10-09 Sun 22:40]
*** DONE Filter common snp not clinvar path
CLOSED: [2022-11-07 Mon 23:00]
Voir [[*common dbSNP not clinvar patho][common dbSNP not clinvar patho]]
*** DONE Filter variant only in consensual sequence
CLOSED: [2022-11-08 Tue 22:23]
*** DONE Filter technical variants
CLOSED: [2022-11-19 Sat 21:34]
*** DONE Utilise AVX pour accélerer l'exécution
CLOSED: [2023-04-29 Sat 15:46]
Sans cela, on a l'avertissement
#+begin_quote
17:28:00.720 INFO  PairHMM - OpenMP multi-threaded AVX-accelerated native PairHMM implementation is not supported
17:28:00.721 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/nix/store/cy9ckxqwrkifx7wf02hm4ww1p6lnbxg9-gatk-4.2.4.1/bin/gatk-package-4.2.4.1-local.jar!/com/intel/gkl/native/libgkl_utils.so
17:28:00.733 WARN  NativeLibraryLoader - Unable to load libgkl_utils.so from native/libgkl_utils.so (/Work/Users/apraga/bisonex/out/NA12878_NIST7035/preprocessing/applybqsr/libgkl_utils821485189051585397.so: libgomp.so.1: cannot open shared object file: No such file or directory)
17:28:00.733 WARN  IntelPairHmm - Intel GKL Utils not loaded
17:28:00.733 WARN  PairHMM - ***WARNING: Machine does not have the AVX instruction set support needed for the accelerated AVX PairHmm. Falling back to the MUCH slower LOGLESS_CACHING implementation!
17:28:00.763 INFO  ProgressMeter - Starting traversal
#+end_quote
libgomp.so est fourni par gcc donc il faut charger le module
 module load gcc@11.3.0/gcc-12.1.0
** KILL Utiliser subworkflow
CLOSED: [2023-04-02 Sun 18:08]
Notre version permet d'être plus souple

023-07-31 Mon 23:09] SCHEDULED: <2023-07-31 Mon>
https://earray.chem.agilent.com/suredesign/index.htm
"Find design"
"Agilent catalog"
Fichiers:
- Regions.bed: Targeted exon intervals, curated and targeted by Agilent Technologies
- MergedProbes.bed: Merged probes for targeted enrichment of exons described in Regions.bed
- Covered.bed: Merged probes and sequences with 95% homology or above
- Padded.bed: Merged probes and sequences with 95% homology or above extended 50 bp at each side
- AllTracks.bed: Targeted regions and covered tracks
 #+begin_src sh
nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/2300346867_63118093_NA12878-GRCh38/callVariant/haplotypecaller/2300346867_63118093_NA12878-GRCh38.vcf.gz --outdir=out/2300346867_63118093_NA12878-GRCh38/happy/ --compare=happy -lib lib --capture=capture/Agilent_SureSelect_All_Exons_v8_hg38_Regions.bed  --id=HG001 --genome=GRCh38
 #+end_src
| 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    |         423 |      395 |       28 |         915 |      108 |       405 |     4 |    13 |      0.933806 |         0.788235 |       0.442623 |        0.854868 |                        |                        |        1.7012987012987013 |        2.7916666666666665 |
| INDEL | PASS   |         423 |      395 |       28 |         915 |      108 |       405 |     4 |    13 |      0.933806 |         0.788235 |       0.442623 |        0.854868 |                        |                        |        1.7012987012987013 |        2.7916666666666665 |
| SNP   | ALL    |       20984 |    20600 |      384 |       26080 |      780 |      4703 |    62 |    10 |        0.9817 |         0.963512 |        0.18033 |        0.972521 |     3.0499710592321048 |     2.7596541786743516 |          1.58256372367935 |        1.8978207694018234 |
| SNP   | PASS   |       20984 |    20600 |      384 |       26080 |      780 |      4703 |    62 |    10 |        0.9817 |         0.963512 |        0.18033 |        0.972521 |     3.0499710592321048 |     2.7596541786743516 |          1.58256372367935 |        1.8978207694018234 |
**** DONE Test Twist Human core Exome (hg38):giab:
CLOSED: [2023-08-01 Tue 23:16] SCHEDULED: <202 3-08-02 Wed>
https://www.twistbioscience.com/resources/data-files/ngs-human-core-exome-panel-bed-file
#+begin_src
nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/2300346867_63118093_NA12878-GRCh38/callVariant/haplotypecaller/2300346867_63118093_NA12878-GRCh38.vcf.gz --outdir=out/2300346867_63118093_NA12878-GRCh38/happy-twist-exome-core/ --compare=happy -lib lib --capture=capture/Twist_Exome_Core_Covered_Targets_hg38.bed  --id=HG001 --genome=GRCh38 -bg
#+end_src
| 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    |         328 |      313 |       15 |         722 |       95 |       309 |     4 |    13 |      0.954268 |         0.769976 |       0.427978 |        0.852273 |                        |                        |        1.8584070796460177 |        2.8967391304347827 |
| INDEL | PASS   |         328 |      313 |       15 |         722 |       95 |       309 |     4 |    13 |      0.954268 |         0.769976 |       0.427978 |        0.852273 |                        |                        |        1.8584070796460177 |        2.8967391304347827 |
| SNP   | ALL    |       19198 |    18962 |      236 |       23381 |      684 |      3738 |    48 |    10 |      0.987707 |         0.965178 |       0.159873 |        0.976313 |     3.1034188034188035 |      2.859264147830391 |        1.5669565217391304 |        1.8578767123287672 |
| SNP   | PASS   |       19198 |    18962 |      236 |       23381 |      684 |      3738 |    48 |    10 |      0.987707 |         0.965178 |       0.159873 |        0.976313 |     3.1034188034188035 |      2.859264147830391 |        1.5669565217391304 |        1.8578767123287672 |
**** DONE Test Twist Human core Exome (hg38):giab:
CLOSED: [2023-08-05 Sat 09:25] SCHEDULED: <2023-08-03 Thu 20:00>
#+begin_src sh
ID="2300346867_NA12878-63118093_S260-GRCh38"; nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/${ID}/callVariant/haplotypecaller/${ID}.vcf.gz --outdir=out/${ID}/happy-twist-exome-core/ --compare=happy -lib lib --capture=capture/Twist_Exome_Core_Covered_Targets_hg38.bed  --id=HG001 --genome=GRCh38 -bg
#+end_src
**** DONE Tester Agilen SureSelect All Exon V8 (hg38) GATK-4.4:giab:
CLOSED: [2023-08-05 Sat 09:25] SCHEDULED: <2023-08-03 Thu 20:00>
**** DONE Vérifier l'impact gatk 4.3 - 4.4 : aucun
CLOSED: [2023-08-05 Sat 09:25]
**** DONE Figure comparant les 3 capture :hg001:
CLOSED: [2023-08-06 Sun 20:24] SCHEDULED: <2023-08-06 Sun>
**** DONE Mail Paul sur  les 3 capture :hg001:
CLOSED: [2023-08-06 Sun 20:24] SCHEDULED: <2023-08-06 Sun>
**** KILL Tester si le panel Twist Alliance VCGS Exome suffit
CLOSED: [2023-07-31 Mon 22:31] SCHEDULED: <2023-07-30 Sun>
**** PROJ Comparer happy et happy-vcfeval :giab:
** TODO Insilico :cento:
*** TODO tous les variants centogène
**** DONE Extraire liste des SNVs
CLOSED: [2023-04-22 Sat 17:32] SCHEDULED: <2023-04-17 Mon>
***** DONE Corriger manquant à la main
CLOSED: [2023-04-22 Sat 17:31]
La sortie est sauvegardé dans git-annex : variants_success.csv
***** DONE Automatique
CLOSED: [2023-04-22 Sat 17:31]
**** DONE Convert SNVs : transcript -> génomique
CLOSED: [2023-06-03 Sat 17:16]
***** DONE Variant_recoder
CLOSED: [2023-04-26 Wed 21:21] SCHEDULED: <2023-04-22 Sat>
****** KILL Haskell: 160 manquant : recoded-success.csv
CLOSED: [2023-04-25 Tue 18:32]
La liste des variants a été générée en Haskel   l et nettoyée à la main.
On générer une liste de variant pour variant_rec            oder et on soumet tout d'un coup.
[[file:~/recherche/bisonex/parsevariants/app/Main.hs][parsevariant]]
#+begin_src haskell
recodeVariant = do
  prepareVariantRecod   er "variant_success.csv" "renamed.csv"
  runVariantRecoder "renamed.csv" "recoded.json"
#+end_src
#+RESULTS:
: <interactive>:4:3-19: error:
:     Variable not in scope: runVariantRecoder :: String -> String -> t
: gh
Problème : 160 n'ont pas pu être lu sur 820, probablement à cause du numéro mineur de transcrit
La sortie est sauvegardé dans git-annex : variants-recoded-raw.json.
****** KILL Julia
CLOSED: [2023-04-25 Tue 18:32]
On regénère la liste de variant et on passe à Julia pour préparer l'appel en parallèle à variant recoder
[[file:~/recherche/bisonex/parsevariants/variantRecoder.jl][variantRecoder.jl]]
#+begin_src julia
setupVariantRecoder(unique(init), n)
#+end_src
Puis
#+begin_src sh
parallel -a parallel-recoder.sh --jobs 10
#+end_src
On récupère les résultats
#+begin_src julia
(fails, success) = mergeVariantRecoder(n)
CSV.write(fSuccess, success)
CSV.write(fFailures, fails)
#+end_src
Certains variants ne sont pas trouvé, donc on prépare un nouveau job en enlevant les versionrs mineures des transcrits
#+begin_src julia
# Cleanup json and txt
if isfile(fSuccess) && isfile(fFailures)
    foreach(rm, variantRecoderInput())
    foreach(rm, variantRecoderOutput())
end
redoFails(fFailures)
#+end_src
Puis
#+begin_src sh
parallel -a parallel-recoder.sh --jobs 3
#+end_src
Il manque encore 70 transcrits
***** DONE Julia avec mobidetails: recode-failures-mobidetails.csv
CLOSED: [2023-04-25 Tue 18:58]
Nouvelle stratégie : on essaie une fois variant recoder.
Pour tous les échecs, on utilise mobidetails (~170).
Si l'ID n'est pas trouvé, on incrémente le numéro de version 2 fois
***** DONE Reste une dizaine à corriger à la main
CLOSED: [2023-04-26 Wed 21:21]
- [X] certains transcrits

023-07-31 Mon 23:09] SCHEDULED: <2023-07-31 Mon>
https://earray.chem.agilent.com/suredesign/index.htm
"Find design"
"Agilent catalog"
Fichiers:
- Regions.bed: Targeted exon intervals, curated and targeted by Agilent Technologies
- MergedProbes.bed: Merged probes for targeted enrichment of exons described in Regions.bed
- Covered.bed: Merged probes and sequences with 95% homology or above
- Padded.bed: Merged probes and sequences with 95% homology or above extended 50 bp at each side
- AllTracks.bed: Targeted regions and covered tracks
 #+begin_src sh
nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/2300346867_63118093_NA12878-GRCh38/callVariant/haplotypecaller/2300346867_63118093_NA12878-GRCh38.vcf.gz --outdir=out/2300346867_63118093_NA12878-GRCh38/happy/ --compare=happy -lib lib --capture=capture/Agilent_SureSelect_All_Exons_v8_hg38_Regions.bed  --id=HG001 --genome=GRCh38
 #+end_src
| 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    |         423 |      395 |       28 |         915 |      108 |       405 |     4 |    13 |      0.933806 |         0.788235 |       0.442623 |        0.854868 |                        |                        |        1.7012987012987013 |        2.7916666666666665 |
| INDEL | PASS   |         423 |      395 |       28 |         915 |      108 |       405 |     4 |    13 |      0.933806 |         0.788235 |       0.442623 |        0.854868 |                        |                        |        1.7012987012987013 |        2.7916666666666665 |
| SNP   | ALL    |       20984 |    20600 |      384 |       26080 |      780 |      4703 |    62 |    10 |        0.9817 |         0.963512 |        0.18033 |        0.972521 |     3.0499710592321048 |     2.7596541786743516 |          1.58256372367935 |        1.8978207694018234 |
| SNP   | PASS   |       20984 |    20600 |      384 |       26080 |      780 |      4703 |    62 |    10 |        0.9817 |         0.963512 |        0.18033 |        0.972521 |     3.0499710592321048 |     2.7596541786743516 |          1.58256372367935 |        1.8978207694018234 |
**** DONE Test Twist Human core Exome (hg38):giab:
CLOSED: [2023-08-01 Tue 23:16] SCHEDULED: <202 3-08-02 Wed>
https://www.twistbioscience.com/resources/data-files/ngs-human-core-exome-panel-bed-file
#+begin_src
nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/2300346867_63118093_NA12878-GRCh38/callVariant/haplotypecaller/2300346867_63118093_NA12878-GRCh38.vcf.gz --outdir=out/2300346867_63118093_NA12878-GRCh38/happy-twist-exome-core/ --compare=happy -lib lib --capture=capture/Twist_Exome_Core_Covered_Targets_hg38.bed  --id=HG001 --genome=GRCh38 -bg
#+end_src
| 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    |         328 |      313 |       15 |         722 |       95 |       309 |     4 |    13 |      0.954268 |         0.769976 |       0.427978 |        0.852273 |                        |                        |        1.8584070796460177 |        2.8967391304347827 |
| INDEL | PASS   |         328 |      313 |       15 |         722 |       95 |       309 |     4 |    13 |      0.954268 |         0.769976 |       0.427978 |        0.852273 |                        |                        |        1.8584070796460177 |        2.8967391304347827 |
| SNP   | ALL    |       19198 |    18962 |      236 |       23381 |      684 |      3738 |    48 |    10 |      0.987707 |         0.965178 |       0.159873 |        0.976313 |     3.1034188034188035 |      2.859264147830391 |        1.5669565217391304 |        1.8578767123287672 |
| SNP   | PASS   |       19198 |    18962 |      236 |       23381 |      684 |      3738 |    48 |    10 |      0.987707 |         0.965178 |       0.159873 |        0.976313 |     3.1034188034188035 |      2.859264147830391 |        1.5669565217391304 |        1.8578767123287672 |
**** DONE Test Twist Human core Exome (hg38):giab:
CLOSED: [2023-08-05 Sat 09:25] SCHEDULED: <2023-08-03 Thu 20:00>
#+begin_src sh
ID="2300346867_NA12878-63118093_S260-GRCh38"; nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/${ID}/callVariant/haplotypecaller/${ID}.vcf.gz --outdir=out/${ID}/happy-twist-exome-core/ --compare=happy -lib lib --capture=capture/Twist_Exome_Core_Covered_Targets_hg38.bed  --id=HG001 --genome=GRCh38 -bg
#+end_src
**** DONE Tester Agilen SureSelect All Exon V8 (hg38) GATK-4.4:giab:
CLOSED: [2023-08-05 Sat 09:25] SCHEDULED: <2023-08-03 Thu 20:00>
**** DONE Vérifier l'impact gatk 4.3 - 4.4 : aucun
CLOSED: [2023-08-05 Sat 09:25]
**** DONE Figure comparant les 3 capture :hg001:
CLOSED: [2023-08-06 Sun 20:24] SCHEDULED: <2023-08-06 Sun>
**** DONE Mail Paul sur  les 3 capture :hg001:
CLOSED: [2023-08-06 Sun 20:24] SCHEDULED: <2023-08-06 Sun>
**** KILL Tester si le panel Twist Alliance VCGS Exome suffit
CLOSED: [2023-07-31 Mon 22:31] SCHEDULED: <2023-07-30 Sun>
**** PROJ Comparer happy et happy-vcfeval :giab:
**** WAIT Mail cento pour demande le type de capture
/Entered on/ [2023-08-07 Mon 20:40]
** TODO Insilico :cento:
*** TODO tous les variants centogène
**** DONE Extraire liste des SNVs
CLOSED: [2023-04-22 Sat 17:32] SCHEDULED: <2023-04-17 Mon>
***** DONE Corriger manquant à la main
CLOSED: [2023-04-22 Sat 17:31]
La sortie est sauvegardé dans git-annex : variants_success.csv
***** DONE Automatique
CLOSED: [2023-04-22 Sat 17:31]
**** DONE Convert SNVs : transcript -> génomique
CLOSED: [2023-06-03 Sat 17:16]
***** DONE Variant_recoder
CLOSED: [2023-04-26 Wed 21:21] SCHEDULED: <2023-04-22 Sat>
****** KILL Haskell: 160 manquant : recoded-success.csv
CLOSED: [2023-04-25 Tue 18:32]
La liste des variants a été générée en Haskel   l et nettoyée à la main.
On générer une liste de variant pour variant_rec            oder et on soumet tout d'un coup.
[[file:~/recherche/bisonex/parsevariants/app/Main.hs][parsevariant]]
#+begin_src haskell
recodeVariant = do
  prepareVariantRecod   er "variant_success.csv" "renamed.csv"
  runVariantRecoder "renamed.csv" "recoded.json"
#+end_src
#+RESULTS:
: <interactive>:4:3-19: error:
:     Variable not in scope: runVariantRecoder :: String -> String -> t
: gh
Problème : 160 n'ont pas pu être lu sur 820, probablement à cause du numéro mineur de transcrit
La sortie est sauvegardé dans git-annex : variants-recoded-raw.json.
****** KILL Julia
CLOSED: [2023-04-25 Tue 18:32]
On regénère la liste de variant et on passe à Julia pour préparer l'appel en parallèle à variant recoder
[[file:~/recherche/bisonex/parsevariants/variantRecoder.jl][variantRecoder.jl]]
#+begin_src julia
setupVariantRecoder(unique(init), n)
#+end_src
Puis
#+begin_src sh
parallel -a parallel-recoder.sh --jobs 10
#+end_src
On récupère les résultats
#+begin_src julia
(fails, success) = mergeVariantRecoder(n)
CSV.write(fSuccess, success)
CSV.write(fFailures, fails)
#+end_src
Certains variants ne sont pas trouvé, donc on prépare un nouveau job en enlevant les versionrs mineures des transcrits
#+begin_src julia
# Cleanup json and txt
if isfile(fSuccess) && isfile(fFailures)
    foreach(rm, variantRecoderInput())
    foreach(rm, variantRecoderOutput())
end
redoFails(fFailures)
#+end_src
Puis
#+begin_src sh
parallel -a parallel-recoder.sh --jobs 3
#+end_src
Il manque encore 70 transcrits
***** DONE Julia avec mobidetails: recode-failures-mobidetails.csv
CLOSED: [2023-04-25 Tue 18:58]
Nouvelle stratégie : on essaie une fois variant recoder.
Pour tous les échecs, on utilise mobidetails (~170).
Si l'ID n'est pas trouvé, on incrémente le numéro de version 2 fois
***** DONE Reste une dizaine à corriger à la main
CLOSED: [2023-04-26 Wed 21:21]
- [X] certains transcrits