Is it possible to suppress the NON_REF tag on variant calls?


In GVCF output from HaplotypeCaller, each line contains the allele, including the lines with explicit variant calls. Is there a simple way to suppress the allele on variant calls?

Also, what is the reason to have a allele on a variant where a specific alternate allele is called?

Thanks for your help.


  • shleeshlee CambridgeMember, Broadie, Moderator
    edited February 2017

    Hi @smottarella,

    Please refer to this document and this doc and links therein for more detailed explanations as to why you want to run HaplotypeCaller in reference confidence mode.

  • Thank you for this information. My question is specific to running HaplotypeCaller in reference confidence mode. I am still not understanding why the NON_REF allele is present on lines that have explicit alternate alleles. In the case of an explicit alternate allele, why are you passing the confidence that at this position my sample is generically not reference (meaning the NON_REF allele) when that same position has a high enough confidence to explicitly call a variant? And again, is there any way to have HaplotypeCaller not return a NON_REF allele on the lines produced in reference confidence mode that already have an explicit alternate allele called, while still providing the NON_REF allele for the blocks that are being called as homozygous reference? I'm finding cases where HaplotypeCaller is callling a genotype that points to NON_REF despite having explicit alternate alleles listed. I'd prefer to only call explicit alleles, and then in the case of homozygous reference, provide the confidence for NON_REF.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    @smottarella When run in GVCF mode, HaplotypeCaller produces a GVCF file, which is an intermediate intended to be further processed by GenotypeGVCFs, as documented in the links above. Once you run this second tool the NONREF tags will go away.
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