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

Assigning per-sample genotypes (HaplotypeCaller) Follow


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    Michael Bradshaw

    Hey GATK maintainers,

    Your equations in LaTeX are not rendering on this page and the "previous step" link in the intro leads to a 404 page. Thought you ought to know.

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    Degang Wu

    Nice article. In addition to the dead link reported by Micahel, I would also like to report that the link to "PL and GQ" is also dead.

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    Huan Fan

    This is one of the most considerate articles I've read about variant calling. 

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