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Does HaplotypeCaller detect SNPs which are heterozygous (not matching the refrence allele)?

Dear GATK team,

I have a simple question regarding the HaplotypeCaller/UnifiedGenotype module. There are 3 options for SNPs in the output depended on the reference.
Homozygous for the reference, heterozygous for the reference and alternate nucleotide and homozygous for the alternate nucleotide (0/0, 1/1, 0/1). But what if I would like to have the SNPs which are heterozygous and do not match the reference allel. So e.g. the reference has an A and the mapped reads indicate a G/T. Does one of the module detect that? I have a diploid species and want to get all SNPs. This issue popped up after I had a look on the output of both modules.

Thanks a lot.


  • JuliaCanitzJuliaCanitz GermanyMember

    Dear GATK team,

    I checked my data again. Unfortunately, I had not looked in detailed on my data. So, I missed that I have multi-allelic sites which are not occurring so often. Sorry for this misunderstanding.

    If someone else has the same question, check your data with grep "1\/2" or "0\/2" beforehand. There is also a GATK command within the SelectVariants which is selecting multi-allelic sites.


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    Hi Julia,

    Thanks for reporting that you figured it out and your solution :smile:


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