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non-reference allele didn't be called into vcf by HC

UniCornUniCorn USMember
edited October 2019 in Ask the GATK team

Hi GATK team

I ran HC joint calling and found out that some non-reference alleles didn't appear in the vcf. Here are how these sites looks like:

Most of these allele have VAF =1 and reside on the region of high sequencing depth with relatively poor alignments (seems to be germline variant).

My first guess is that they are disgarded by early steps of HC. However, I went through documentation of HC procedure and didn't find a definitive answer of how exactly they are discarded. Can anyone share some insights on this? Thanks a lot


  • UniCornUniCorn USMember

    Can anyone share some insights on this? Really appreciate

  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Hi @UniCorn can you produce a bamout and provide an IGV screenshot of the sites you question?
    See the doc and CTRL find --bam-output to understand how you can group by artificial haplotype and see how HC's graph assembly step has impacted calling. HaplotypeCaller will utilize soft-clipped sequences towards realignment, which is different than BWA mem. Hopefully the reassembled region will show you the support used by HC to make the call.

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