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

FilterMutectCalls htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Invalid GZIP header

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    Bhanu Gandham

    HI Jenifer

    Seems like there is an issue with your input vcf.

    1. Can you please confirm that your input vcf is infact gzipped and not truncatted? Maybe try unzipping and gzipping your input vcf again.
    2. Can you please run ValidateVariants to ensure that the input vcf is not malformed?
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