seen variant in a genome browser doesn't appear in vcf file, using HaplotypeCaller
Hi GATK team,
I ran HaplotypeCaller on a bam file that I pre-pprocessed according to your Best-Practices.
When looking in a genome browser at this bam, I encountered a position that seems to have a variant, but the variant doesn't appear in the vcf file.
This is the line from the vcf file (the variant I'm talking about is at position 75680995):
3 75680992 . C . . END=75680995 GT:DP:GQ:MIN_DP:PL 0/0:155:0:147:0,0,0
Attached is the picture from the genome browser - At the same position (75680995) there is a variant with the allele 'A', while the reference is 'C'. The coverage at this position is 195, and 171 of those reads are for the 'A' allele.
Why is this happen?