Hi all,
I have the below variant from samtools mpileup and annotated as 1/1
which means homozygous for the alternate allele.
chr1 11580049 . A T 6.19 .
DP=291;VDB=0.0000;AF1=1;AC1=2;DP4=82,13,2,1;MQ=11;FQ=-260;PV4=0.37,1,1,0.017
GT:PL:GQ 1/1:38,233,0:48
However, the DP4 column shows there are 95 reads for reference and 3
reads for alternate allele. Could someone comment on this snp being
reported as homozygous for alternate allele despite of having very few
reads supporting it.
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