simple question about CombineVariants

BogdanBogdan Palo Alto, CAMember

Dear all,

when you have time, would appreciate please a piece of advice about the CombineVariants : I aim to integrate 2 vcf files, one is from MUTECt2, the other is from Strelka. If I see correctly the output, CombineVariants adds a few extra-fields to the merged file (below). May I ask about the meaning/interpretation of these fields in the output MERGED file (AC=1;AF=0.250;AN=4) ? Is there any way to prevent their addition ? thanks !


chr21 5148899 . C A . PASS ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=8.71;TLOD=29.85 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:36,16:0.308:9:7:0.438:816,374:11:25 0/0:29,0:0.00:0:0:.:702,0:13:16


chr21 5148899 . C A . PASS NT=ref;QSS=47;QSS_NT=47;SGT=CC->AC;SOMATIC;TQSS=1;TQSS_NT=1 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 33:0:0:0:0,0:33,33:0,0:0,0 57:0:0:0:19,20:38,39:0,0:0,0

In the merged file :

chr21 5148899 . C A . PASS AC=1;AF=0.250;AN=4;ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=8.71;NT=ref;QSS=47;QSS_NT=47;SGT=CC->AC;SOMATIC;TLOD=29.85;TQSS=1;TQSS_NT=1;set=Intersection GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/0:29,0:0.00:0:0:.:702,0:13:16 0/1:36,16:0.308:9:7:0.438:816,374:11:25

The command I used is :

$GATK -T CombineVariants \
--variant:strelka vcf-strelka.vcf \
--variant:mutect2 vcf-mutect2.vcf \
-o vcf-combine.vcf \
-genotypeMergeOptions PRIORITIZE \
-priority mutect2,strelka \

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