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 genotype mode


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    David Benjamin

    Stefano Lise There is not a mode to call only the given alleles and disable discovery of any other variation.  However, if your concern is compute time you can use the same VCF as both the --alleles argument and the -L (intervals) argument.

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