A sample variant from my vcf file :
I 27000 . A G 37.88 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;MQ=6.53;MQ0=49;QD=0.74 GT:ADP:GQ:PL 1/1:37,14:51:6.01:69,6,0
which gives DP=51 but while visualizing the variant on IGV i'm getting
Total Count as 56. Seems like some reads have been disqualified for calling variant and the number is lesser in vcf than the bam file.
I need to understand this discrepancy. I would like to view same counts while in vcf and in viewer.
I 27000 . A G 37.88 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;MQ=6.53;MQ0=49;QD=0.74 GT:ADP:GQ:PL 1/1:37,14:51:6.01:69,6,0
which gives DP=51 but while visualizing the variant on IGV i'm getting
Total Count as 56. Seems like some reads have been disqualified for calling variant and the number is lesser in vcf than the bam file.
I need to understand this discrepancy. I would like to view same counts while in vcf and in viewer.
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