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

JAVA errors from gnomad resource in Mutect2



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    David Benjamin

    Akshay Sanghi Please use the official GATK resources gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf (hg19/b37) and gs://gatk-best-practices/somatic-hg38/af-only-gnomad.hg38.vcf.gz (hg38)

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    Akshay Sanghi

    Thank you for the reply. Is the af-only-gnomad.hg38 file from gnomAD version 3? It would be great to use gnomADv3 because I am doing whole genome analysis and version 3 has much more whole genome data. If gnomADv3 wasn't used to make the af-only file, could you please share the workflow to generate the af-only file?


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