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

GATK Mutect2 fail to call variant



  • Avatar
    David Benjamin

    yangjw GATK tools are often shaky with amplicon data, which we don't officially support.  Using --linked-de-bruijn-graph and -downsampling-stride is the right thing to do. My guess is that with 50000x coverage something goes wrong in assembly, but with Mutect3 coming out soon I would not have time to diagnose it, unfortunately.

    You should also turn on mitochondria mode.

    For filtering, we recommend FilterMutectCalls.  Mutect2 is not designed to be run without it.  The best thing to do is run the entire best practices somatic small variants pipeline.

    It is odd that the PGTs are the same for the first two variants you show because they seem to be out of phase.  The PGT comes from code shared with HaplotypeCaller and it can be faulty.  I would just ignore it.

    Comment actions Permalink
  • Avatar

    Hi, David, thank you for your reply and advice!

    Well, I haven't figure out what exactly cause 16507G missing. Because the other variants are called correctly and none of them is missing. I guess maybe 16507G has something special which disturb the Mutect2 calling. I will adopt your advice and go on to find a better solution.

    As for the PGT issue, at present I still filter such variants with AF, and the results are consist with the known reference sample. Thanks to you, I decide not to worry much about such PGTs.

    Thank you again. Looking forward to Mutect3 coming! 

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk