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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

Does CollectReadCounts Count Fragments or Individual Reads?

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    Genevieve Brandt (she/her)

    Hi Fong Chun Chan,

    The CollectReadCounts tool collects reads, not fragments. It did replace the CollectFragmentCounts tool but the output will be twice as many as CollectFragmentCounts because it is different.

    I'll put in a documentation request for this, thanks for bringing it to our attention!

    Best,

    Genevieve

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    Fong Chun Chan

    Thanks Genevieve.

    Do you know if it is possible to count fragments using the CollectReadCounts or know of another GATK tool that can do this?

    Kind regards,

    Fong

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    Genevieve Brandt (she/her)

    Fong Chun Chan what do you need the fragment count for? It would be easier to give a recommendation if you give a background for what you are trying to do.

    This CollectReadCounts tool counts how many reads overlap each of the input intervals.

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