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

GATK ModelSegments result

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    Tamar Melman

    Hi Indrani, I hope I can answer some of your questions. 

    1. A log2 copy ratio of -29.999 is equivalent to a copy ratio of 2^-29.99999, or close to 0. This almost certainly indicates a homozygous deletion. 

    2. You'll probably want posterior 50; this is equivalent to the median of all denoised copy ratios included in that segment. 

    3. For mapping segments to genes you'll want to run FuncotateSegments. This takes in a `--segments` argument which requires output from CallCopyRatioSegments, which is downstream of ModelSegments. So the workflow would be: ModelSegments -> CallCopyRatioSegments -> FuncotateSegments. 

    To see how we typically slot these tools into a production pipeline, see https://github.com/broadinstitute/gatk/blob/master/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl

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    Tamar Melman

    Indrani, One thing to add to point 2: if you run CallCopyRatioSegments, you will get a clearer output with mean log2 copy ratio (as opposed to posterior 50) along with the call for that segment (amplification, deletion, or neutral). 

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    Indrani Datta

    Thank you so much for the detail explanation. I will work on these and get back to you if there is anything else comes up.

    Indrani

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