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

Parameter tuning in Mutect2

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    David Benjamin

    Are you running FilterMutectCalls and are you looking only at PASS variants in IGV?  The normal_artifact filter, which is applied by FilterMutectCalls, should handle this without any need to modify parameters.

    If you are running FilterMutectCalls already, could you post your full command lines, the GATK version (eg 4.1.5.0), and paste a few VCF lines with variants that should be filtered but are not?

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