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 filter somatic mutations as multiallelic and clustered_events

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    David Benjamin

    You can adjust the -max-events-in-region and -max-alt-allele-count arguments.  However, alleles filtered by these are overwhelmingly likely to be false positives.  I'm not disagreeing with you when it comes to known hotspots, but I am saying that relaxing these filters will greatly elevate the false positive rate across the genome.  

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    Nesrine

    -max-alt-allele-count is already fixed to 1. I changed -max-events-in-region which was fixed to 2  and unfortunately, I've had the same results...

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