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MGHComputationalPathology / CellTics

Center for Integrated Diagnostics at Mass General Hospital NGS tools
BSD 3-Clause "New" or "Revised" License
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Issue with when using single thread #16

Open sybrohee opened 1 year ago

sybrohee commented 1 year ago

When working with only one thread (i.e. --threads = 1), the results are different from the results obtained with more than one thread. Indeed, the "original variants" are altered (GROUP_ID is filled in, IN_GROUP stays empty) and the sample fields are all set to 0 while the "merged variants" are added (with relevant IN_GROUP). When working in multithreaded mode, I have the expected results : no alteration of the original variant (IN_GROUP is filled in, GROUP_ID stays empty) and addition of the "merged variants" (with relevant IN_GROUP).

#### SINGLE THREAD (???)

chrX    19754920    rs7883332   C   G   11731.8 PASS    Info1=3;Info2=6;Info3=info3elem1,info3elem2,info3elem3;GROUP_ID=;IN_GROUP=chrX_19754920_0;ALT_AF=0.0;ALT_DP=0.0;PRIMARY_CALLER=vargrouper;REF_DP=0.0    GT:DP:AD:AF:GQ  ./.:.:.:.:.
chrX    19754926    rs773922290 G   T   11683.8 PASS    Info1=3;Info2=6;Info3=info3elem1,info3elem2,info3elem3;GROUP_ID=;IN_GROUP=chrX_19754920_0   GT:DP:AD:AF:GQ  0/1:1163:827,336:0.288908:99

chrX    19754920    rs7883332   cgaactg GgaactT 11707.8 .   Info1=3;Info2=6;Info3=info3elem1,info3elem2,info3elem3;GROUP_ID=;IN_GROUP=chrX_19754920_0;ALT_AF=0.0;ALT_DP=0.0;PRIMARY_CALLER=vargrouper;REF_DP=0.0    GT:DP:AD:AF:GQ  ./.:.:.:.:.

##### MUTLTI THREAD (EXPECTED BEHAVIOUR)

chrX    19754920    rs7883332   C   G   11731.8 PASS    Info1=3;Info2=6;Info3=info3elem1,info3elem2,info3elem3;GROUP_ID=;IN_GROUP=chrX_19754920_0   GT:DP:AD:AF:GQ  0/1:1157:816,341:0.294728:99
chrX    19754926    rs773922290 G   T   11683.8 PASS    Info1=3;Info2=6;Info3=info3elem1,info3elem2,info3elem3;GROUP_ID=;IN_GROUP=chrX_19754920_0   GT:DP:AD:AF:GQ  0/1:1163:827,336:0.288908:99

chrX    19754920    rs7883332   cgaactg GgaactT 11707.8 .   Info1=3;Info2=6;Info3=info3elem1,info3elem2,info3elem3;GROUP_ID=chrX_19754920_0;IN_GROUP=;ALT_AF=0.0;ALT_DP=0.0;PRIMARY_CALLER=vargrouper;REF_DP=0.0    GT:DP:AD:AF:GQ  ./.:.:.:.:.