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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

GetPileupSummaries following Mutect2: what inputs are suitable for --intervals (-L)?



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    Brian Haas


    Good question.  If you're using whole exome data and have an intervals file, I think you should use that for the -L parameter, but use the common variants vcf for the -V option.

    If you're doing whole genome sequencing, then using the same parameter for -L and -V is likely most appropriate.

    (Other GATK folks, please correct me if that's wrong... )



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    Thank you for confirming Brian Haas - much appreciated. I imagine that for targeted sequencing panels the intervals file can be used for the -L parameter also, if it can be for whole exome data.

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