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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

BedToIntervalList and IntervalListTools: can interval lists without unique names for intervals be used?

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    Genevieve Brandt (she/her)

    Hi ISmolicz,

    I am going to move your post into our Community Discussions -> Documentation Questions topic, as the "Other" topic is for reporting bugs and issues with GATK.

    You can read more about our forum guidelines and the topics here: Forum Guidelines.

    Best,

    Genevieve

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    Genevieve Brandt (she/her)

    ISmolicz With what GATK tools will you be using the interval list?

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    ISmolicz

    Thank you for your reply Genevieve Brandt.

    At present, I am using an interval list with the following GATK tools: GenomicsDBImport, Mutect2, GetPileupSummaries and DepthOfCoverage.

    In addition, I use an interval list with the following Picard tools: CollectSequencingArtifactMetrics, CollectHsMetrics (two separate lists) and CollectVariantCallingMetrics.

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    Genevieve Brandt (she/her)

    Have there been any warning messages or issues with those tools and the interval list without unique names?

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