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

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Somatic copy number variant discovery (CNVs) Follow

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Derek Caetano-Anolles
  • Updated

Purpose

Identify somatic copy number variant (CNVs) in a case sample. Requires an appropriate Panel of Normals (PON).

Reference Implementations

Pipeline Summary Notes Github Terra
Somatic CNV case sample Case BAM to CNV universal yes b37
Somatic CNV PON creation Normal BAMs to PON universal yes b37

Documentation for these workflows is in development.

Related articles

3 comments

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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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    Laurent MANCHON

    i have only a tumor bam file and a pon.hdf5 and no normal library
    Is it possible to use this pipeline ?
    I'm looking for a bash pipeline with all the GATK commands to find the CNV, is it available somewhere ?

    thank you --

     

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    Besher Tabbara
    • Edited

    You will need to have target intervals or bins in addition to the bam in order to collect read counts. For exomes you can take the interval list that corresponds to the capture targets specific to manufacturer's exome prep kit and add some padding using the PreprocessIntervals command.

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