search

broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
Other
1.69k stars 588 forks source link

germline CNV #4790

Closed wujh2017 closed 6 years ago

wujh2017 commented 6 years ago

I have got my result using 32 samples.but there is a problem that too many variants in the "sample_x_genotyped_segments.vcf" which i don't expect,it has 24987 vairants.So what happend and what should i do ? it's my samples' problem or i just need to filter the vcf file ?

FORMAT=

FORMAT=

FORMAT=

FORMAT=

FORMAT=<ID=QS,Number=1,Type=Integer,Description="Complementary Phred-scaled probability that at least one point (i.e. target or bin) in the segment agrees with the segment copy-number call, divid

FORMAT=

FORMAT=

GATKCommandLine=<ID=PostprocessGermlineCNVCalls,CommandLine="PostprocessGermlineCNVCalls --calls-shard-path ../GermlineCNVCaller/COHORTtest-calls --model-shard-path ../GermlineCNVCaller/COHORT

INFO=

source=PostprocessGermlineCNVCalls

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT R32

chr1 14363 CNV_chr1_14363_16765 N , . . END=16765 GT:CN:NP:QA:QS:QSE:QSS 1:1:4:35:23:25:64 chr1 16858 CNV_chr1_16858_17055 N , . . END=17055 GT:CN:NP:QA:QS:QSE:QSS 1:0:1:25:25:25:25 chr1 17233 CNV_chr1_17233_17742 N , . . END=17742 GT:CN:NP:QA:QS:QSE:QSS 1:1:2:49:38:49:25 chr1 69091 CNV_chr1_69091_70008 N , . . END=70008 GT:CN:NP:QA:QS:QSE:QSS 1:0:1:272:272:272:272 chr1 661140 CNV_chr1_661140_665184 N , . . END=665184 GT:CN:NP:QA:QS:QSE:QSS 2:4:1:3:3:3:3 chr1 761587 CNV_chr1_761587_763155 N , . . END=763155 GT:CN:NP:QA:QS:QSE:QSS 0:2:2:18:35:16:70 chr1 783034 CNV_chr1_783034_789740 N , . . END=789740 GT:CN:NP:QA:QS:QSE:QSS 2:3:5:12:6:30:11 chr1 803453 CNV_chr1_803453_812182 N , . . END=812182 GT:CN:NP:QA:QS:QSE:QSS 2:5:3:14:7:28:19 chr1 852953 CNV_chr1_852953_861393 N , . . END=861393 GT:CN:NP:QA:QS:QSE:QSS 0:2:6:50:17:50:49 chr1 865535 CNV_chr1_865535_871276 N , . . END=871276 GT:CN:NP:QA:QS:QSE:QSS 2:4:3:13:5:28:14 chr1 874420 CNV_chr1_874420_892653 N , . . END=892653 GT:CN:NP:QA:QS:QSE:QSS 0:2:25:45:12:72:44 chr1 894309 CNV_chr1_894309_896180 N , . . END=896180 GT:CN:NP:QA:QS:QSE:QSS 2:4:3:12:5:34:13 chr1 896673 CNV_chr1_896673_1182102 N , . . END=1182102 GT:CN:NP:QA:QS:QSE:QSS 0:2:130:10:12:22:39 chr1 1189294 CNV_chr1_1189294_1209234 N , . . END=1209234 GT:CN:NP:QA:QS:QSE:QSS 2:4:8:3:3:8:16 chr1 1219358 CNV_chr1_1219358_1278138 N , . . END=1278138 GT:CN:NP:QA:QS:QSE:QSS 0:2:85:20:12:31:10 chr1 1284276 CNV_chr1_1284276_1293915 N , . . END=1293915 GT:CN:NP:QA:QS:QSE:QSS 2:3:11:7:6:7:14 chr1 1309110 CNV_chr1_1309110_1356650 N , . . END=1356650 GT:CN:NP:QA:QS:QSE:QSS 0:2:25:22:13:48:7 chr1 1361508 CNV_chr1_1361508_1376145 N , . . END=1376145 GT:CN:NP:QA:QS:QSE:QSS 2:4:5:10:5:24:12 chr1 1385069 CNV_chr1_1385069_1412730 N , . . END=1412730 GT:CN:NP:QA:QS:QSE:QSS 0:2:13:7:13:24:50 chr1 1414024 CNV_chr1_1414024_1414488 N , . . END=1414488 GT:CN:NP:QA:QS:QSE:QSS 1:1:2:23:14:35:28 chr1 1416247 CNV_chr1_1416247_1417994 N , . . END=1417994 GT:CN:NP:QA:QS:QSE:QSS 2:4:3:10:4:29:10 chr1 1420396 CNV_chr1_1420396_1452792 N , . . END=1452792 GT:CN:NP:QA:QS:QSE:QSS 0:2:11:28:15:30:40 chr1 1453096 CNV_chr1_1453096_1453155 N , . . END=1453155 GT:CN:NP:QA:QS:QSE:QSS 1:0:1:37:37:37:37 chr1 1454301 CNV_chr1_1454301_1480382 N , . . END=1480382 GT:CN:NP:QA:QS:QSE:QSS 0:2:18:29:15:8:44 chr1 1500153 CNV_chr1_1500153_1510262 N , . . END=1510262 GT:CN:NP:QA:QS:QSE:QSS 2:4:2:2:2:13:2 chr1 1550884 CNV_chr1_1550884_1564102 N , . . END=1564102 GT:CN:NP:QA:QS:QSE:QSS 0:2:16:21:10:15:22 chr1 1564513 CNV_chr1_1564513_1567753 N , . . END=1567753 GT:CN:NP:QA:QS:QSE:QSS 2:3:5:7:5:7:15 chr1 1571695 CNV_chr1_1571695_1576474 N , . . END=1576474 GT:CN:NP:QA:QS:QSE:QSS 0:2:9:16:7:21:7 chr1 1577267 CNV_chr1_1577267_1577362 N , . . END=1577362 GT:CN:NP:QA:QS:QSE:QSS 1:0:1:238:238:238:238 chr1 1592940 CNV_chr1_1592940_1608285 N , . . END=1608285 GT:CN:NP:QA:QS:QSE:QSS 2:3:8:10:4:11:15 chr1 1623888 CNV_chr1_1623888_1624243 N , . . END=1624243 GT:CN:NP:QA:QS:QSE:QSS 2:5:1:4:4:4:4 chr1 1632800 CNV_chr1_1632800_1639684 N , . . END=1639684 GT:CN:NP:QA:QS:QSE:QSS 0:2:10:13:12:17:14 chr1 1640477 CNV_chr1_1640477_1640572 N , . . END=1640572 GT:CN:NP:QA:QS:QSE:QSS 1:0:1:266:266:266:266 chr1 1650798 CNV_chr1_1650798_1655705 N , . . END=1655705 GT:CN:NP:QA:QS:QSE:QSS 2:4:3:3:2:13:4 chr1 1663681 CNV_chr1_1663681_1756938 N , . . END=1756938 GT:CN:NP:QA:QS:QSE:QSS 0:2:27:8:15:6:12 chr1 1770629 CNV_chr1_1770629_1770677 N , . . END=1770677 GT:CN:NP:QA:QS:QSE:QSS 2:4:1:1:1:1:1 chr1 1846266 CNV_chr1_1846266_1850527 N , . . END=1850527 GT:CN:NP:QA:QS:QSE:QSS 0:2:10:24:16:29:6 chr1 1884752 CNV_chr1_1884752_1888223 N , . . END=1888223 GT:CN:NP:QA:QS:QSE:QSS 2:4:2:8:5:2:9 chr1 1890559 CNV_chr1_1890559_1935276 N , . . END=1935276 GT:CN:NP:QA:QS:QSE:QSS 2:3:16:1:4:21:2 chr1 1956381 CNV_chr1_1956381_1962192 N , . . END=1962192 GT:CN:NP:QA:QS:QSE:QSS 0:2:8:23:11:27:23

samuelklee commented 6 years ago

Hi @wujh2017,

You should filter your variants using the various quality scores described in the VCF header. We find that simply filtering on QS is typically a good strategy.

Also, you might find it more helpful to post this sort of question in the GATK forums---other users might benefit from seeing the answer there.