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GenotypeGVCFs output with additional annotation

lh15lh15 SangerMember

Hi there,

Thank you guys for developing & maintaining such a good software!
I'm actually just starting to use GATK with Haplotypecaller. For me, there's a very useful annotation "StrandBiasBySample" or "StrandAlleleCountsBySample" that gives all the alignment information for a variant. It can be generated by HC, but after joint genotyping, it's just gone.
There is a previous post asking about how to add this annotation to the final vcf, and Sheila mentioned she's already put in a request for adding this.
So I'm just wandering, have you guys fixed this in one of the nighty build?

Many Thanks!!!

Best Answer

Answers

  • lh15lh15 SangerMember

    @Geraldine_VdAuwera said:
    I'm pretty sure this was put in a week ago -- I was on vacation but I think I remember it go into github.

    IIRC only HC can annotate SAC initially (VA cannot) but from now on GenotypeGVCFs will carry it over to the final VCF if it is present in the GVCFs.

    Thanks, Geraldine, that's really good to know! I'm just gonna try it out.

  • tommycarstensentommycarstensen United KingdomMember ✭✭✭

    To anyone reading this thread. It's continued here:

    http://gatkforums.broadinstitute.org/discussion/5265/
    
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