Hi
With HaplotypeCaller,Version=2.8-1-g932cd3a
In the raw VCF we are seeing instances of
GT:AD:DP:GQ:PL 0/1:22,0:22:53:53,0,2067
A HET call (0/1) but there are no ALT reads (22,0)
Some Questions to clarify
a) Is this VCF format valid?
b) Is this intended or bug?
c) Are there current process that would filter these entries?
i) We've tried SelectVariants with --ExcludeNonVariants but the entries are still there
ii) Would downstream steps such as variant recalibration/filter catch these?
More Technical details:
This was run using Queue,
I've attached the VCF, I'm assuming the Command line information in the VCF header is sufficient?
Regions of interest (I've been greping for ",0:" )
chr2 212543723
chr3 10088443
If this is a bug. Let me know if you would like me to provide some bams
Thanks