Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Missing mutation in VCF output from GenotypeGVCFs


1 comment

  • Avatar
    Pamela Bretscher


    This does seem like somewhat of a strange output. This variant appears to be called as a no-call (GT of ./.) in the VCF. Given that you have really high depth at this site, with a majority of reference calls but also a significant number of non-reference calls, GenotypeGVCFs may be throwing out this variant because it does not know how to call it. This article may help provide some more information. Are there other variants that you are not seeing in the output of GenotypeGVCFs? 

    Kind regards,


    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk