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# Combine variants from different tools

Posts: 17Member

Hi,

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.

EXAMPLE:

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


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


  
combined.vcf:
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:

  
combined.vcf:
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


Tagged:

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

Geraldine Van der Auwera, PhD

• Posts: 17Member

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

Daniel.

• Posts: 17Member

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

Daniel.