B:BD[
3.33265] → [
3.33265:33678]
∅:D[
3.33678] → [
5.40054:40251]
B:BD[
5.40054] → [
5.40054:40251]
B:BD[
5.40251] → [
6.9576:17247]
B:BD[
6.17247] → [
2.8557:8774]
LED: <2023-10-10 Tue>
**** DONE En T2T avec liftover (filtre = spip) : ok mais lent et trop de variants :tests:
CLOSED: [2023-09-17 Sun 17:13] 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: vé
rifié 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
Annotation spip *très lente* : 1h13 !
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 0 missed variants
Et on a trop de variants en sortie (7330 !)
**** DONE Mail Paul avec résultats filtre en T2T + nouveau schéma
CLOSED: [2023-09-17 Sun 23:15] SCHEDULED: <2023-09-17 Sun>
* Ré-interprétation
** PROJ Lancer tests sur données brutes [127/250]
- [X] 100222_63015289
- [X] 1600304839_63051311
- [X] 1900007827_62913191
- [X] 1900398899_62999500
- [X] 1900486799_62913197
- [X] 2100422923_62952677
- [X] 2100458888_62933047
- [X] 2100601558_62903840
- [X] 2100609288_62905768
- [X] 2100609501_62905776
- [X] 2100614493_62951074
- [X] 2100622566_62908067
- [X] 2100622601_62908060
- [X] 2100622705_62908063
- [X] 2100640027_62911936
- [X] 2100645285_62913212
- [X] 2100661411_62914081
- [X] 2100661462_62914086
- [X] 2100708257_62921596
- [X] 2100738732_62926501
- [X] 2100738850_62926509
- [X] 2100746751_62926505
- [X] 2100746797_62926506
- [X] 2100782349_62931722
- [X] 2100782416_62931561
- [X] 2100782559_62931718
- [X] 2100799204_62934768
- [X] 2200010202_62940284
- [X] 2200023600_62940631
- [X] 2200024348_62999591
- [X] 2200027505_62942457
- [X] 2200038776_62943412
- [X] 2200041919_62943405
- [X] 2200088014_62951326
- [X] 2200146652_62959388
- [X] 2200151850_62960953
- [X] 2200160014_62959475
- [X] 2200160070_62959478
- [X] 2200201368_62967471
- [X] 2200201400_62967470
- [X] 2200265558_62976332
- [X] 2200265605_62976401
- [X] 2200267046_62975192
- [X] 2200273878_62999530
- [X] 2200279708_62977002
- [X] 2200284408_62979102
- [X] 2200293987_62979116
- [X] 2200294359_62979118
- [X] 2200306299_62982217
- [X] 2200306539_62982193
- [X] 220030671_62982211
- [X] 2200307058_62982231
- [X] 2200307108_62982196
- [X] 2200307136_62982221
- [X] 2200307199_62982239
- [X] 2200307230_62982234
- [X] 2200307262_62982219
- [X] 2200307297_62982227
- [X] 2200324510_62985453
- [X] 2200324549_62985478
- [X] 2200324573_62985445
- [X] 2200324594_62985467
- [X] 2200324606_62985463
- [X] 2200324614_62985459
- [X] 2200338306_62985430
- [X] 2200343880_62989407
- [X] 2200343910_62989460
- [X] 2200343938_62989451
- [X] 2200343966_62989456
- [X] 2200343993_62989440
- [X] 2200344013_62989464
- [X] 2200349749_62989465
- [X] 2200363462_62988848
- [X] 2200377880_62991993
- [X] 2200378032_62991991
- [X] 2200383996_62993828
- [X] 2200384015_62993796
- [X] 2200384046_62993822
- [X] 2200384117_62993808
- [X] 2200384187_62993825
- [X] 2200384231_62992898
- [X] 2200385658_63060260
- [X] 2200394260_62994732
- [X] 2200395817_62994742
- [X] 2200396731_62994737
- [X] 2200424073_62999579
- [X] 2200424207_62999632
- [X] 2200426178_62999630
- [X] 2200426243_62999635
- [X] 2200426466_62999605
- [X] 2200426642_62999627
- [X] 2200427406_62999649
- [X] 2200427512_62999639
- [X] 2200428953_62999572
- [X] 2200428981_62999600
- [X] 2200428999_62999592
- [X] 2200441970_63000868
- [X] 2200441989_63000882
- [X] 2200442135_63000864
- [X] 2200442216_63000886
- [X] 2200442257_63000951
- [X] 2200451801_63003573
- [X] 2200451862_63004218
- [X] 2200451894_63004210
- [X] 2200456165_63051294
- [X] 2200459865_63004933
- [X] 2200459968_63004937
- [X] 2200460073_63004943
- [X] 2200460121_63004684
- [X] 2200467051_63003856
- [X] 2200467225_63004940
- [X] 2200467261_63004930
- [X] 2200467338_63004925
- [X] 2200470099_63004485
- [X] 2200470142_63004480
- [X] 2200471780_63004362
- [X] 2200480910_63006466
- [X] 2200495073_63010427
- [X] 2200495510_63009152
- [X] 2200508677_63060252
- [X] 2200510531_63012582
- [X] 2200510628_63012549
- [X] 2200510657_63012554
- [X] 2200511249_63012533
- [X] 2200511274_63012586
- [X] 2200517952_63060399
- [X] 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_63061874
- [ ] 2300055421_63061871
- [ ] 2300055440_63061880
- [ ] 230006894_63064950
- [ ] 2300071111_63070356
- [ ] 2300083434_63071675
- [ ] 2300103609_63076239
- [ ] 2300104572_63076232
- [ ] 2300109602_63076765
- [ ] 2300109665_63076770
- [ ] 2300119721_63078732
- [ ] 2300137773_63078133
- [ ] 2300137834_63078123
- [ ] 2300167821_63086183
- [ ] 2300172698_63113453
- [ ] 2300188216_63090609
- [ ] 2300188281_63090632
- [ ] 2300188800_63090616
- [ ] 2300193193645_63090623
- [ ] 2300193668_63090611
- [ ] 2300195426_63090608
- [ ] 2300201017_63089636
- [ ] 2300227479_63098330
- [ ] 2300232688_63130821
- [ ] 2300292749_63109239
- [ ] 230029277_63109247
- [ ] 2300294712_63109236
- [ ] 2300308032_63111581
- [ ] 2300323537_63114209
- [ ] 2300334609_63115535
- [ ] 2300346867_63118093
- [ ] 2300346867_63118093_NA12878
- [ ] 2300348940_63118099
- [ ] 2300359806_63119915
- [ ] 2300380476_63123963
- [ ] 2300382582_63123749
- [ ] 2300384269_63126867
- [ ] 2300407581_63130826
- [ ] 2300407626_63130842
- [ ] 2300409593_63130874
- [ ] 2300409612_63130980
- [ ] 2300417623_63131524
* Résultats
** TODO
Speed-up BWA-mem
SCHEDULED: <2023-10-08 Sun>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-10-08 Sun>
* Communication
** TODO Mail NGS-diag
SCHEDULED: <2023-10-06 Fri>
/Entered on/ [2023-10-04 Wed 19:33]
LED: <2023-10-10 Tue>
**** DONE En T2T avec liftover (filtre = spip) : ok mais lent et trop de variants :tests:
CLOSED: [2023-09-17 Sun 17:13] 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
Annotation spip *très lente* : 1h13 !
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 0 missed variants
Et on a trop de variants en sortie (7330 !)
**** DONE Mail Paul avec résultats filtre en T2T + nouveau schéma
CLOSED: [2023-09-17 Sun 23:15] SCHEDULED: <2023-09-17 Sun>
* Ré-interprétation
** PROJ Lancer tests sur données brutes [146/250]
- [X] 100222_63015289
- [X] 1600304839_63051311
- [X] 1900007827_62913191
- [X] 1900398899_62999500
- [X] 1900486799_62913197
- [X] 2100422923_62952677
- [X] 2100458888_62933047
- [X] 2100601558_62903840
- [X] 2100609288_62905768
- [X] 2100609501_62905776
- [X] 2100614493_62951074
- [X] 2100622566_62908067
- [X] 2100622601_62908060
- [X] 2100622705_62908063
- [X] 2100640027_62911936
- [X] 2100645285_62913212
- [X] 2100661411_62914081
- [X] 2100661462_62914086
- [X] 2100708257_62921596
- [X] 2100738732_62926501
- [X] 2100738850_62926509
- [X] 2100746751_62926505
- [X] 2100746797_62926506
- [X] 2100782349_62931722
- [X] 2100782416_62931561
- [X] 2100782559_62931718
- [X] 2100799204_62934768
- [X] 2200010202_62940284
- [X] 2200023600_62940631
- [X] 2200024348_62999591
- [X] 2200027505_62942457
- [X] 2200038776_62943412
- [X] 2200041919_62943405
- [X] 2200088014_62951326
- [X] 2200146652_62959388
- [X] 2200151850_62960953
- [X] 2200160014_62959475
- [X] 2200160070_62959478
- [X] 2200201368_62967471
- [X] 2200201400_62967470
- [X] 2200265558_62976332
- [X] 2200265605_62976401
- [X] 2200267046_62975192
- [X] 2200273878_62999530
- [X] 2200279708_62977002
- [X] 2200284408_62979102
- [X] 2200293987_62979116
- [X] 2200294359_62979118
- [X] 2200306299_62982217
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- [X] 2200324510_62985453
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- [X] 2200324594_62985467
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- [X] 2200324614_62985459
- [X] 2200338306_62985430
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- [X] 2200343910_62989460
- [X] 2200343938_62989451
- [X] 2200343966_62989456
- [X] 2200343993_62989440
- [X] 2200344013_62989464
- [X] 2200349749_62989465
- [X] 2200363462_62988848
- [X] 2200377880_62991993
- [X] 2200378032_62991991
- [X] 2200383996_62993828
- [X] 2200384015_62993796
- [X] 2200384046_62993822
- [X] 2200384117_62993808
- [X] 2200384187_62993825
- [X] 2200384231_62992898
- [X] 2200385658_63060260
- [X] 2200394260_62994732
- [X] 2200395817_62994742
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- [X] 2200426243_62999635
- [X] 2200426466_62999605
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- [X] 2200427406_62999649
- [X] 2200427512_62999639
- [X] 2200428953_62999572
- [X] 2200428981_62999600
- [X] 2200428999_62999592
- [X] 2200441970_63000868
- [X] 2200441989_63000882
- [X] 2200442135_63000864
- [X] 2200442216_63000886
- [X] 2200442257_63000951
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- [X] 2200460121_63004684
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- [X] 2200467261_63004930
- [X] 2200467338_63004925
- [X] 2200470099_63004485
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- [X] 2200471780_63004362
- [X] 2200480910_63006466
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- [X] 2200511274_63012586
- [X] 2200517952_63060399
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- [X] 2200524009_63014044
- [ ] 2200524609_63014046
- [X] 2200524616_63014048
- [X] 2200533429_63060425
- [X] 2200539735_63060406
- [X] 2200549908_63019339
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- [X] 2200569969_63019991
- [X] 2200570001_63021580
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- [X] 2200570035_63021491
- [ ] 2200570042_63021493
- [ ] 2200570050_63021494
- [ ] 2200579897_63024910
- [ ] 2200583995_63024866
- [ ] 2200584035_63024905
- [ ] 2200584069_63024888
- [ ] 2200584126_63024810
- [ ] 2200589507_63026712
- [ ] 2200597365_63027994
- [ ] 2200597480_63027988
- [ ] 2200597752_63026853
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- [ ] 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_63061874
- [ ] 2300055421_63061871
- [ ] 2300055440_63061880
- [ ] 230006894_63064950
- [ ] 2300071111_63070356
- [ ] 2300083434_63071675
- [ ] 2300103609_63076239
- [ ] 2300104572_63076232
- [ ] 2300109602_63076765
- [ ] 2300109665_63076770
- [ ] 2300119721_63078732
- [ ] 2300137773_63078133
- [ ] 2300137834_63078123
- [ ] 2300167821_63086183
- [ ] 2300172698_63113453
- [ ] 2300188216_63090609
- [ ] 2300188281_63090632
- [ ] 2300188800_63090616
- [ ] 2300193193645_63090623
- [ ] 2300193668_63090611
- [ ] 2300195426_63090608
- [ ] 2300201017_63089636
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- [ ] 2300232688_63130821
- [ ] 2300292749_63109239
- [ ] 230029277_63109247
- [ ] 2300294712_63109236
- [ ] 2300308032_63111581
- [ ] 2300323537_63114209
- [ ] 2300334609_63115535
- [ ] 2300346867_63118093
- [ ] 2300346867_63118093_NA12878
- [ ] 2300348940_63118099
- [ ] 2300359806_63119915
- [ ] 2300380476_63123963
- [ ] 2300382582_63123749
- [ ] 2300384269_63126867
- [ ] 2300407581_63130826
- [ ] 2300407626_63130842
- [ ] 2300409593_63130874
- [ ] 2300409612_63130980
- [ ] 2300417623_63131524
* Résultats
** TODO Speed-up BWA-mem
SCHEDULED: <2023-10-08 Sun>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-10-08 Sun>
* Communication
** DONE Mail NGS-diag
CLOSED: [2023-10-06 Fri 08:04] SCHEDULED: <2023-10-06 Fri>
/Entered on/ [2023-10-04 Wed 19:33]