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

Is it ok to use -L for each chromosome separately when running Mutect2?


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    David Benjamin

    Xuning Wang Sure, that approach is fine and will give the same results as calling on the whiole genome.  The stats files can be combined with `MergeMutectStats`.  This is the exactly the approach that the official Mutect2 WDL in the GATK github repo uses.

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