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

How to find or generate common germline variant sites VCF required by GetPileupSummaries

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    David Benjamin

    You can find it in our best practices google bucket.  Depending on your reference, gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf or gs://gatk-best-practices/somatic-hg38/small_exac_common_3.hg38.vcf.gz (the accompanying VCF indices are also there).

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    Antti Koskenalho

    David, thank you very much for confirming this!

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