: [2023-08-20 Sun 09:18] SCHEDULED: <2023-08-20 Sun>
***** DONE Vérifier après filterpolymorphis : 0 perdus en plus
CLOSED: [2023-08-20 Sun 09:18] SCHEDULED: <2023-08-20 Sun>
***** DONE Vérifier après filter vep: 2 perdus en plus
CLOSED: [2023-08-20 Sun 12:37] SCHEDULED: <2023-08-20 Sun>
2×3 DataFrame
Row │ varian
t meanQual depth
│ String Float64 Int64
─────┼─────────────────────────────────────
1 │ chr17:g.7852503T>C 60.0 96
2 │ chrX:g.47575255G>A 60.0 145
***** DONE 1ere correction spip: meilleur nombre de variants en sortie mais manque toujours ces 2
CLOSED: [2023-08-20 Sun 11:38]
***** DONE --pick : résout le problème
CLOSED: [2023-08-20 Sun 12:37]
chrX:g.47575255G>A est rendu downstream_gene_variant avec l'option --pick
Or il n'est pas en5' dans les transcrits refseq...
https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chrX%3A47575242%2D47575268&hgsid=301211823_xpelPqPJije7wSIhg070JeGH5ZwV
https://mobidetails.iurc.montp.inserm.fr/MD/api/variant/238296/browser/
Idem pour l'autre
chr17:g.7852503T>C
https://mobidetails.iurc.montp.inserm.fr/MD/api/variant/182993/browser/
Note:
VEP chooses one block of annotation per variant, using an ordered set of criteria. This order may be customised using --pick_order.
MANE Select transcript status
MANE Plus Clinical transcript status
canonical status of transcript
APPRIS isoform annotation
transcript support level
biotype of transcript ("protein_coding" preferred)
CCDS status of transcript
consequence rank according to this table
translated, transcript or feature length (longer preferred)
"Wherever possible we would discourage you from summarising data in this way. "
**** DONE Mail alexis
CLOSED: [2023-08-20 Sun 13:45] SCHEDULED: <2023-08-20 Sun>
**** TODO Données simuscop 200x
SCHEDULED: <2023-09-24 Sun>
**** TODO En T2T avec liftover (nouveau filtre = spip ou splice ai selon génome) :tests:
SCHEDULED: <2023-09-17 Sun >
Conversion en bed
#+begin_src sh :dir:~/code/sanger
open snvs-cento-sanger.csv | select chrom pos | insert pos2 {$in.pos } | to csv --separator="\t" | save snvs-cento-sanger.bed -f
#+end_src
Test position 1 : rien dans le VCF
* Ré-interprétation
** TODO Lancer tests sur données brutes [3/250]
- [X] 100222_63015289
- [X] 1600304839_63051311
- [X] 1900007827_62913191
- [ ] 1900398899_62999500
- [ ] 1900486799_62913197
- [ ] 2100422923_62952677
- [ ] 2100458888_62933047
- [ ] 2100601558_62903840
- [ ] 2100609288_62905768
- [ ] 2100609501_62905776
- [ ] 2100614493_62951074
- [ ] 2100622566_62908067
- [ ] 2100622601_62908060
- [ ] 2100622705_62908063
- [ ] 2100640027_62911936
- [ ] 2100645285_62913212
- [ ] 2100661411_62914081
- [ ] 2100661462_62914086
- [ ] 2100708257_62921596
- [ ] 2100738732_62926501
- [ ] 2100738850_62926509
- [ ] 2100746751_62926505
- [ ] 2100746797_62926506
- [ ] 2100782349_62931722
- [ ] 2100782416_62931561
- [ ] 2100782559_62931718
- [ ] 2100799204_62934768
- [ ] 2200010202_62940284
- [ ] 2200023600_62940631
- [ ] 2200024348_62999591
- [ ] 2200027505_62942457
- [ ] 2200038776_62943412
- [ ] 2200041919_62943405
- [ ] 2200088014_62951326
- [ ] 2200146652_62959388
- [ ] 2200151850_62960953
- [ ] 2200160014_62959475
- [ ] 2200160070_62959478
- [ ] 2200201368_62967471
- [ ] 2200201400_62967470
- [ ] 2200265558_62976332
- [ ] 2200265605_62976401
- [ ] 2200267046_62975192
- [ ] 2200273878_62999530
- [ ] 2200279708_62977002
- [ ] 2200284408_62979102
- [ ] 2200293987_62979116
- [ ] 2200294359_62979118
- [ ] 2200306299_62982217
- [ ] 2200306539_62982193
- [ ] 220030671_62982211
- [ ] 2200307058_62982231
- [ ] 2200307108_62982196
- [ ] 2200307136_62982221
- [ ] 2200307199_62982239
- [ ] 2200307230_62982234
- [ ] 2200307262_62982219
- [ ] 2200307297_62982227
- [ ] 2200324510_62985453
- [ ] 2200324549_62985478
- [ ] 2200324573_62985445
- [ ] 2200324594_62985467
- [ ] 2200324606_62985463
- [ ] 2200324614_62985459
- [ ] 2200338306_62985430
- [ ] 2200343880_62989407
- [ ] 2200343910_62989460
- [ ] 2200343938_62989451
- [ ] 2200343966_62989456
- [ ] 2200343993_62989440
- [ ] 2200344013_62989464
- [ ] 2200349749_62989465
- [ ] 2200363462_62988848
- [ ] 2200377880_62991993
- [ ] 2200378032_62991991
- [ ] 2200383996_62993828
- [ ] 2200384015_62993796
- [ ] 2200384046_62993822
- [ ] 2200384117_62993808
- [ ] 2200384187_62993825
- [ ] 2200384231_62992898
- [ ] 2200385658_63060260
- [ ] 2200394260_62994732
- [ ] 2200395817_62994742
- [ ] 2200396731_62994737
- [ ] 2200424073_62999579
- [ ] 2200424207_62999632
- [ ] 2200426178_62999630
- [ ] 2200426243_62999635
- [ ] 2200426466_62999605
- [ ] 2200426642_62999627
- [ ] 2200427406_62999649
- [ ] 2200427512_62999639
- [ ] 2200428953_62999572
- [ ] 2200428981_62999600
- [ ] 2200428999_62999592
- [ ] 2200441970_63000868
- [ ] 2200441989_63000882
- [ ] 2200442135_63000864
- [ ] 2200442216_63000886
- [ ] 2200442257_63000951
- [ ] 2200451801_63003573
- [ ] 2200451862_63004218
- [ ] 2200451894_63004210
- [ ] 2200456165_63051294
- [ ] 2200459865_63004933
- [ ] 2200459968_63004937
- [ ] 2200460073_63004943
- [ ] 2200460121_63004684
- [ ] 2200467051_63003856
- [ ] 2200467225_63004940
- [ ] 2200467261_63004930
- [ ] 2200467338_63004925
- [ ] 2200470099_63004485
- [ ] 2200470142_63004480
- [ ] 2200471780_63004362
- [ ] 2200480910_63006466
- [ ] 2200495073_63010427
- [ ] 2200495510_63009152
- [ ] 2200508677_63060252
- [ ] 2200510531_63012582
- [ ] 2200510628_63012549
- [ ] 2200510657_63012554
- [ ] 2200511249_63012533
- [ ] 2200511274_63012586
- [ ] 2200517952_63060399
- [ ] 2200519525_63060439
- [ ] 2200524009_63014044
- [ ] 2200524609_63014046
- [ ] 2200524616_63014048
- [ ] 2200533429_63060425
- [ ] 2200539735_63060406
- [ ] 2200549908_63019339
- [ ] 2200549965_63019349
- [ ] 2200550414_63019357
- [ ] 2200550471_63020031
- [ ] 2200550490_63019351
- [ ] 2200550505_63019340
- [ ] 2200555565_63018614
- [ ] 2200559438_63020029
- [ ] 2200559682_63020030
- [ ] 2200559713_63019623
- [ ] 2200559739_63019626
- [ ] 2200569969_63019991
- [ ] 2200570001_63021580
- [ ] 2200570025_63021490
- [ ] 2200570035_63021491
- [ ] 2200570042_63021493
- [ ] 2200570050_63021494
- [ ] 2200579897_63024910
- [ ] 2200583995_63024866
- [ ] 2200584035_63024905
- [ ] 2200584069_63024888
- [ ] 2200584126_63024810
- [ ] 2200589507_63026712
- [ ] 2200597365_63027994
- [ ] 2200597480_63027988
- [ ] 2200597752_63026853
- [ ] 2200597778_63027992
- [ ] 22005977_63026903
- [ ] 2200609031_63026527
- [ ] 2200614198_63113928
- [ ] 2200620372_63030821
- [ ] 2200620442_63030810
- [ ] 2200620498_63030816
- [ ] 2200620628_63031031
- [ ] 2200622310_63030984
- [ ] 2200622355_63030956
- [ ] 2200625369_63028699
- [ ] 2200625410_63028697
- [ ] 2200625536_63028694
- [ ] 2200630189_63030665
- [ ] 2200635149_63033182
- [ ] 2200644544_63037731
- [ ] 2200644594_63037725
- [ ] 2200650089_63038093
- [ ] 2200666292_63076568
- [ ] 2200669188_63036688
- [ ] 2200669320_63040259
- [ ] 2200669383_63040254
- [ ] 2200669414_63040257
- [ ] 2200669446_63040251
- [ ] 2200680342_63105271
- [ ] 2200694535_63042853
- [ ] 2200694789_63042862
- [ ] 2200694858_63042702
- [ ] 2200694917_63042696
- [ ] 2200699290_63043047
- [ ] 2200699345_63040238
- [ ] 2200699383_63043050
- [ ] 2200699412_63040731
- [ ] 220071551_63048935
- [ ] 2200731515_63048963
- [ ] 2200748145_63051198
- [ ] 2200748171_63051213
- [ ] 2200751046_63051249
- [ ] 2200751101_63051234
- [ ] 2200766471_63054590
- [ ] 2200767731_63054595
- [ ] 2200767822_63054464
- [ ] 2200775505_63060410
- [ ] 2200850441_63019345
- [ ] 220597589_63026879
- [ ] 2300003253_63060430
- [ ] 2300005679_63060370
- [ ] 2300009914_63060390
- [ ] 2300028784_63060001
- [ ] 2300036815_63063357
- [ ] 2300055382_63
: [2023-08-20 Sun 09:18] SCHEDULED: <2023-08-20 Sun>
***** DONE Vérifier après filterpolymorphis : 0 perdus en plus
CLOSED: [2023-08-20 Sun 09:18] SCHEDULED: <2023-08-20 Sun>
***** DONE Vérifier après filter vep: 2 perdus en plus
CLOSED: [2023-08-20 Sun 12:37] SCHEDULED: <2023-08-20 Sun>
2×3 DataFrame
Row │ variant meanQual depth
│ String Float64 Int64
─────┼─────────────────────────────────────
1 │ chr17:g.7852503T>C 60.0 96
2 │ chrX:g.47575255G>A 60.0 145
***** DONE 1ere correction spip: meilleur nombre de variants en sortie mais manque toujours ces 2
CLOSED: [2023-08-20 Sun 11:38]
***** DONE --pick : résout le problème
CLOSED: [2023-08-20 Sun 12:37]
chrX:g.47575255G>A est rendu downstream_gene_variant avec l'option --pick
Or il n'est pas en5' dans les transcrits refseq...
https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chrX%3A47575242%2D47575268&hgsid=301211823_xpelPqPJije7wSIhg070JeGH5ZwV
https://mobidetails.iurc.montp.inserm.fr/MD/api/variant/238296/browser/
Idem pour l'autre
chr17:g.7852503T>C
https://mobidetails.iurc.montp.inserm.fr/MD/api/variant/182993/browser/
Note:
VEP chooses one block of annotation per variant, using an ordered set of criteria. This order may be customised using --pick_order.
MANE Select transcript status
MANE Plus Clinical transcript status
canonical status of transcript
APPRIS isoform annotation
transcript support level
biotype of transcript ("protein_coding" preferred)
CCDS status of transcript
consequence rank according to this table
translated, transcript or feature length (longer preferred)
"Wherever possible we would discourage you from summarising data in this way. "
**** DONE Mail alexis
CLOSED: [2023-08-20 Sun 13:45] SCHEDULED: <2023-08-20 Sun>
**** TODO Données simuscop 200x
SCHEDULED: <2023-09-24 Sun>
**** TODO En T2T avec liftover (nouveau filtre = spip ou splice ai selon génome) :tests:
SCHEDULED: <2023-09-17 Sun>
1. Conversion en bed
#+begin_src sh :dir:~/code/sanger
open snvs-cento-sanger.csv | select chrom pos | insert pos2 {$in.pos } | to csv --separator="\t" | save snvs-cento-sanger.bed -f
#+end_src
2. Liftover avec UCSC (en ligne)
NB: vérifié sur le premier résultat en cherche le read contenant le variant (samtools view -r puis samtools view | grep en T2T) et avec l'aide d'IGV, on a un variant qui correspond en
chr1:10757746
3. En supposant que l'ordre des variants n'a pas changé, on ajoute simplement REF et ALT avec annotateLifted.jl
Résultat:
2×3 DataFrame
Row │ variant meanQual depth
│ String Float64 Int64
─────┼──────────────────────────────────────
1 │ chr12:g.13594572 60.0 1
2 │ chr17:g.10204026 60.0 1
144 found over 146
filter depth : another 0 missed variants
filter poly : another 0 missed variants
filter vep : another 4 missed variants
4×3 DataFrame
Row │ variant meanQual depth
│ String Float64 Int64
─────┼───────────────────────────────────────
1 │ chr10:g.130884530 60.0 67
2 │ chr10:g.240362 60.0 79
3 │ chr14:g.52665581 60.0 51
4 │ chr19:g.41325390 60.0 180
* Ré-interprétation
** TODO Lancer tests sur données brutes [6/250]
- [X] 100222_63015289
- [X] 1600304839_63051311
- [X] 1900007827_62913191
- [X] 1900398899_62999500
- [X] 1900486799_62913197
- [X] 2100422923_62952677
- [ ] 2100458888_62933047
- [ ] 2100601558_62903840
- [ ] 2100609288_62905768
- [ ] 2100609501_62905776
- [ ] 2100614493_62951074
- [ ] 2100622566_62908067
- [ ] 2100622601_62908060
- [ ] 2100622705_62908063
- [ ] 2100640027_62911936
- [ ] 2100645285_62913212
- [ ] 2100661411_62914081
- [ ] 2100661462_62914086
- [ ] 2100708257_62921596
- [ ] 2100738732_62926501
- [ ] 2100738850_62926509
- [ ] 2100746751_62926505
- [ ] 2100746797_62926506
- [ ] 2100782349_62931722
- [ ] 2100782416_62931561
- [ ] 2100782559_62931718
- [ ] 2100799204_62934768
- [ ] 2200010202_62940284
- [ ] 2200023600_62940631
- [ ] 2200024348_62999591
- [ ] 2200027505_62942457
- [ ] 2200038776_62943412
- [ ] 2200041919_62943405
- [ ] 2200088014_62951326
- [ ] 2200146652_62959388
- [ ] 2200151850_62960953
- [ ] 2200160014_62959475
- [ ] 2200160070_62959478
- [ ] 2200201368_62967471
- [ ] 2200201400_62967470
- [ ] 2200265558_62976332
- [ ] 2200265605_62976401
- [ ] 2200267046_62975192
- [ ] 2200273878_62999530
- [ ] 2200279708_62977002
- [ ] 2200284408_62979102
- [ ] 2200293987_62979116
- [ ] 2200294359_62979118
- [ ] 2200306299_62982217
- [ ] 2200306539_62982193
- [ ] 220030671_62982211
- [ ] 2200307058_62982231
- [ ] 2200307108_62982196
- [ ] 2200307136_62982221
- [ ] 2200307199_62982239
- [ ] 2200307230_62982234
- [ ] 2200307262_62982219
- [ ] 2200307297_62982227
- [ ] 2200324510_62985453
- [ ] 2200324549_62985478
- [ ] 2200324573_62985445
- [ ] 2200324594_62985467
- [ ] 2200324606_62985463
- [ ] 2200324614_62985459
- [ ] 2200338306_62985430
- [ ] 2200343880_62989407
- [ ] 2200343910_62989460
- [ ] 2200343938_62989451
- [ ] 2200343966_62989456
- [ ] 2200343993_62989440
- [ ] 2200344013_62989464
- [ ] 2200349749_62989465
- [ ] 2200363462_62988848
- [ ] 2200377880_62991993
- [ ] 2200378032_62991991
- [ ] 2200383996_62993828
- [ ] 2200384015_62993796
- [ ] 2200384046_62993822
- [ ] 2200384117_62993808
- [ ] 2200384187_62993825
- [ ] 2200384231_62992898
- [ ] 2200385658_63060260
- [ ] 2200394260_62994732
- [ ] 2200395817_62994742
- [ ] 2200396731_62994737
- [ ] 2200424073_62999579
- [ ] 2200424207_62999632
- [ ] 2200426178_62999630
- [ ] 2200426243_62999635
- [ ] 2200426466_62999605
- [ ] 2200426642_62999627
- [ ] 2200427406_62999649
- [ ] 2200427512_62999639
- [ ] 2200428953_62999572
- [ ] 2200428981_62999600
- [ ] 2200428999_62999592
- [ ] 2200441970_63000868
- [ ] 2200441989_63000882
- [ ] 2200442135_63000864
- [ ] 2200442216_63000886
- [ ] 2200442257_63000951
- [ ] 2200451801_63003573
- [ ] 2200451862_63004218
- [ ] 2200451894_63004210
- [ ] 2200456165_63051294
- [ ] 2200459865_63004933
- [ ] 2200459968_63004937
- [ ] 2200460073_63004943
- [ ] 2200460121_63004684
- [ ] 2200467051_63003856
- [ ] 2200467225_63004940
- [ ] 2200467261_63004930
- [ ] 2200467338_63004925
- [ ] 2200470099_63004485
- [ ] 2200470142_63004480
- [ ] 2200471780_63004362
- [ ] 2200480910_63006466
- [ ] 2200495073_63010427
- [ ] 2200495510_63009152
- [ ] 2200508677_63060252
- [ ] 2200510531_63012582
- [ ] 2200510628_63012549
- [ ] 2200510657_63012554
- [ ] 2200511249_63012533
- [ ] 2200511274_63012586
- [ ] 2200517952_63060399
- [ ] 2200519525_63060439
- [ ] 2200524009_63014044
- [ ] 2200524609_63014046
- [ ] 2200524616_63014048
- [ ] 2200533429_63060425
- [ ] 2200539735_63060406
- [ ] 2200549908_63019339
- [ ] 2200549965_63019349
- [ ] 2200550414_63019357
- [ ] 2200550471_63020031
- [ ] 2200550490_63019351
- [ ] 2200550505_63019340
- [ ] 2200555565_63018614
- [ ] 2200559438_63020029
- [ ] 2200559682_63020030
- [ ] 2200559713_63019623
- [ ] 2200559739_63019626
- [ ] 2200569969_63019991
- [ ] 2200570001_63021580
- [ ] 2200570025_63021490
- [ ] 2200570035_63021491
- [ ] 2200570042_63021493
- [ ] 2200570050_63021494
- [ ] 2200579897_63024910
- [ ] 2200583995_63024866
- [ ] 2200584035_63024905
- [ ] 2200584069_63024888
- [ ] 2200584126_63024810
- [ ] 2200589507_63026712
- [ ] 2200597365_63027994
- [ ] 2200597480_63027988
- [ ] 2200597752_63026853
- [ ] 2200597778_63027992
- [ ] 22005977_63026903
- [ ] 2200609031_63026527
- [ ] 2200614198_63113928
- [ ] 2200620372_63030821
- [ ] 2200620442_63030810
- [ ] 2200620498_63030816
- [ ] 2200620628_63031031
- [ ] 2200622310_63030984
- [ ] 2200622355_63030956
- [ ] 2200625369_63028699
- [ ] 2200625410_63028697
- [ ] 2200625536_63028694
- [ ] 2200630189_63030665
- [ ] 2200635149_63033182
- [ ] 2200644544_63037731
- [ ] 2200644594_63037725
- [ ] 2200650089_63038093
- [ ] 2200666292_63076568
- [ ] 2200669188_63036688
- [ ] 2200669320_63040259
- [ ] 2200669383_63040254
- [ ] 2200669414_63040257
- [ ] 2200669446_63040251
- [ ] 2200680342_63105271
- [ ] 2200694535_63042853
- [ ] 2200694789_63042862
- [ ] 2200694858_63042702
- [ ] 2200694917_63042696
- [ ] 2200699290_63043047
- [ ] 2200699345_63040238
- [ ] 2200699383_63043050
- [ ] 2200699412_63040731
- [ ] 220071551_63048935
- [ ] 2200731515_63048963
- [ ] 2200748145_63051198
- [ ] 2200748171_63051213
- [ ] 2200751046_63051249
- [ ] 2200751101_63051234
- [ ] 2200766471_63054590
- [ ] 2200767731_63054595
- [ ] 2200767822_63054464
- [ ] 2200775505_63060410
- [ ] 2200850441_63019345
- [ ] 220597589_63026879
- [ ] 2300003253_63060430
- [ ] 2300005679_63060370
- [ ] 2300009914_63060390
- [ ] 2300028784_63060001
- [ ] 2300036815_63063357
- [ ] 2300055382_63