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GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Combine variants from different tools


I'm working with different tools to call variants (GATK is one of them) for the same sample and I'm merging these results with

gatk -T CombineVariants -R ucsc.hg19.fasta -V:GATK GATK.vcf -V:OTHER OTHER.vcf -o combined.vcf -genotypeMergeOptions PRIORITIZE --rod_priority_list GATK,OTHER

But when I have a discrepancy between results (I mean, same chr and pos, but different call), I just get GATK's result in my result file, Is there any way to have both calls when I have discrepancies?
I don't want to use -genotypeMergeOptions UNIQUIFY.


chr17   7917905 .       C       T       360.16  .       [...]   GT     0/1
chr17   7918012 .       C       T       896.16  .       [...]  GT     0/1

chr17   7917905 .       C       T       360.16  .       [...]   GT     0/1
chr17   7918012 .       C       T       896.16  .       [...]  GT     1/1

chr17   7917905 .       C       T       360.16  .       [...];set=Intersection   GT     0/1
chr17   7918012 .       C       T       896.16  .       [...];set=Intersection  GT     0/1

What I want to obtain:

chr17   7917905 .       C       T       360.16  .       [...];set=Intersection   GT     0/1
chr17   7918012 .       C       T       896.16  .       [...];set=GATK  GT     0/1
chr17   7918012 .       C       T       896.16  .       [...];set=OTHER  GT     1/1

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Check out the available options for the --genotypeMergeOptions argument.

  • I did it, I was trying with all of the possibilities and neither of them works for me.


  • I was expecting something more "automatized", but I don't see other option, Thanks!


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    This is the area of the GATK domain where it is still more a programming framework more than a toolbox, ie there is a limited number of things that you can do automagically/ out of the box. But as time goes we add capabilities, and we're also going to be putting together a cookbook of recipes for these kinds of things, so hopefully in time we will meet needs such as these better. It's always good to know what kind of things people want to do "in the wild" as opposed to our little aquarium, of course.

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