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

Somatic copy number variant discovery (CNVs) Follow

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    Andrew Cherniack

    Where can we find a description on what all of the outputs of the somatic copy number pipeline are?

    In particular we want to know what each of these seg files are:

    allele_fraction_legacy_segments_tumor
    called_copy_ratio_legacy_segments_tumor
    called_copy_ratio_segments_tumor
    copy_ratio_legacy_segments_tumor
    copy_ratio_only_segments_tumor
    modeled_segments_begin_tumor
    modeled_segments_tumor
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