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

SOLVED: Get read counts of Mutect2 somatic variants


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    Mariana E. M.


    I realized that this information is actually contained in the VCF file as allele depth (AD), reporting the number of reads supporting the reference and alternative allele. The identifier (AD) is in the column "FORMAT" and its value in the subsequent column.

    Details can also be found in the GATK documentation about VCF files.

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