Het calls from HaplotypeCaller with no ALT reads
Posted in Ask the GATK team | Last updated on 2014-01-22 04:02:46

Comments (1)


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


Return to top Comment on this article in the forum