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 CNV pipeline segmentation with custom het list?

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    Pamela Bretscher

    Hi Qing Zhang,

    As far as I know, there isn't a way to run ModelSegments with your own het file (i.e. without the genotyping step). However, you can tweak parameters such as minimum-total-allele-count, genotyping-homozygous-log-ratio-threshold, and genotyping-homozygous-log-ratio-threshold when running ModelSegments to change the requirements and way that hets are defined. Descriptions of these options can be found in the ModelSegments Tool Documentation. Do you think that adjusting these parameters would allow you to get closer to your intended set of hets?

    Kind regards,

    Pamela

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    Qing Zhang

    Thanks Pamela.

    After some discussion with Sam on slack, I think we are going to do this by replacing "allelic-counts" with custom hets genotypes by ourselves, set all filtering criteria to be as lenient as possible, e.g. setting minimum-total-allele-count-case minimum-total-allele-count-normal to be ~10, and increasing genotyping-homozygous-log-ratio-threshold to be 0. However, I have not got around to test this idea — I will let you know if this works as we’d expect!

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    Pamela Bretscher

    Hi Qing Zhang,

    Thank you for posting this potential solution here as it may help other users in the same situation and please update with your results!

    Kind regards,

    Pamela

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