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

Which file is af-only-gnomad.hg38.vcf.gz?

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    David Benjamin

    rohit satyam The gnomAD VCF is enormous because it contains a lot of INFO field annotations, none of which Mutect2 needs except for AF (allele frequency in the population).  The AF only gnomad that we provide in the best practices google bucket is the gnomAD VCF with all extraneous annotations removed.  In principle you could use gnomAD with all the annotations, but it would waste a lot of CPU time parsing the VCF.

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    rohit satyam

    Wow. Thanks a lot. David Benjamin

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