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CombineVariants -> FilteredInAll


I do not know if this is desired behavior or bug in CombineVariants. However CombineVariants doesn't behave like l would like it to.

I tried to merge two vcf files (a.vcf and b.vcf) and afterwards select variants that are unique to one file (=variants which are present only in a.vcf). The problem is that CombineVariants reports "FilteredInAll" if variant is filtered in a.vcf and completely missing from b.vcf! In my opinion CombineVariants should report "FilteredIn[a.vcf]". For me "FilteredInAll" sounds like variant is present in both files (a.vcf and b.vcf) but filtered.

If this is not bug but desired behavior could someone tell me how to find unique variants despite of value in FILTER field?

I am using GATK version 2.3-9-ge5ebf34 on linux (x86_64)




  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Teemu,

    That is the desired behavior. It would be possible to create a mode to do what you want but we don't have the resources to do it ourselves right now. We're happy to look at a patch, though, if you implement it yourself.

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