Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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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

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    Pamela Bretscher

    Hi,

    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,

    Pamela

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