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

merge nearby variants in vcf from mutect2

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    Pamela Bretscher

    Hi Junfeng Jiang,

    Have you verified that these variants are from the same sample and are phased properly? I'm not sure why the tool would output three separate deletions that are all in a row when it could output one deletion. If everything has been done properly, then I don't believe there is a GATK tool that would achieve what you are looking for.

    Kind regards,

    Pamela

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