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Het calls from HaplotypeCaller with no ALT reads
In the raw VCF we are seeing instances of
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:" )
If this is a bug. Let me know if you would like me to provide some bams