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

GetPileupSummaries get only header and no output

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    Genevieve Brandt (she/her)

    Hi xiaotian shen,

    We can try to figure this out! The tool returned "SUCCESS", so that is good!

    It looks like a lot of your reads were filtered out. How many reads did you start with?

    Genevieve

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