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

Mutect2 with HiFi

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    Daphna

    Sorry, small typo:
    "about variants" should be "about 100 variants" 

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    James Emery

    Hello Daphna. Sorry to hear that HiFi reads are performing poorly in Mutect2. We designed and have generally tested Mutect2 and HaplotypeCaller to be run with Illumina reads and that it is entirely possible we are mishandling HiFi reads somewhere in our engine. Most likely if you are seeing absolutely no variants called at all from the tool M2 is silently filtering out all of the reads/failing to assemble them correctly for whatever reason. We expect to at least see some variants coming out of the tool on the HiFi reads assuming that they are of a reasonable quality/coverage.

    Could you post the log output from your M2 run? at the bottom of that should be an accounting of the read filters that were applied and that should give us an idea of what the tool is rejecting about your HiFi reads. If that still doesn't work there are some subsequent steps that would be worth testing on here: https://gatk.broadinstitute.org/hc/en-us/articles/360043491652-When-HaplotypeCaller-and-Mutect2-do-not-call-an-expected-variant. 

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