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

Asking for advice on Mutect2 calling in somatic but amplicon data



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    David Benjamin

    yangjw Using the --linked-de-bruijn-graph argument might improve accuracy and if you're lucky it will reduce the CPU cost enough to turn off or at least reduce downsampling.

    It's also worth trying to use the --downsampling-stride argument.  There's no harm in setting it as large as 50 and this might smooth out the downsampling.

    I wouldn't worry about differences in unfiltered Mutect2 output.  You should always run FilterMutectCalls (or better yet, run the entire pipeline using our best practices WDL script) on the raw output of Mutect2.

    Finally, in most cases it is best to keep soft-clipped bases.

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    Hi, David, thank you for your reply. I set the '--downsampling-stride 50'  and get the ideal result. Your advice helps me a lot! Thank you again!


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