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

Introducing DRAGMAP, the new genome mapper in DRAGEN-GATK Follow


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    Reference masking is not an innovation but a necessity and a well known practice for years. Giab released v2 for hg38. Shortcomings quassi solved by dragmap cannot be called innovation. I am wondering about the results of a comparison where none of the maskable regions apply with a reference genome like hs37d5.

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    Kevin Esoh

    Hi Derek, thanks for this very informative post.

    Just wondering whether the open source DRAGMAP is automatically alternate aware. I am asking because it appears some of the features for hash table generation published on illumina's website such as --ht-alt-liftover and –ht alt-aware-validate=false are not present in DRAGMAP.

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