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

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4 comments

  • Hello, 

    In the case of using hg19 human reference, where can I find a panel of normals similar to 1000g_pon.hg38.vcf to pass to this method?

    Best Regards, Manuel

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    Niharika

    Can this tool be used to call variants from multiple samples? By multiple samples I mean multiple individuals.

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    Qi Yu

    Hi, could you modify the code example from

    `--mitochondria`

    To

    `--mitochondria-mode` 

    Since `mitochondria is not a recognized option`.

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    Maia Malonzo

    Hi, Can Mutect2 be used with RNA-seq data?

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