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

Muect2 is running till Chr1 and there no stats file


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    David Benjamin

    This looks like an error due to an ill-formed germline resource file.  Perhaps it is missing the AF field somewhere.  Rather than debug it, we always recommend using our best practices resource file: gs://gatk-best-practices/somatic-hg38/af-only-gnomad.hg38.vcf.gz

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