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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

Difference between GATK Germline CNV Pipeline vs Genome STRiP?

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    Genevieve Brandt (she/her)

    Bob Handsaker can provide insight about GenomeSTRiP.

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    Muhammad Shoaib Akhtar

    Dear Brandt, Thank you for referral. Can you please tell me if using GATK I may get absolute copy numbers?

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    Bob Handsaker

    Compared to other methods, I would say that Genome STRiP is particularly good at utilizing normalized depth-of-coverage and multi-allelic CNVs that can be best detected based on this. The LCNV pipeline is also rather unique in trying to assess large, potentially mosaic CNVs from read depth, although tools like mocha are generally better powered.

     

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    Genevieve Brandt (she/her)

    Hi Muhammad Shoaib Akhtar, the denoised copy ratio with GATK germline CNV can be used as an absolute copy number when multiplied by 2.

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    Muhammad Shoaib Akhtar

    Thank you so much.

    May I know how I can make contig ploidy priors table needed to run DetermineGermlineContigPloidy?

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    Genevieve Brandt (she/her)

    Hi Muhammad Shoaib Akhtar,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

    Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

    We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

    For context, check out our support policy.

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    Muhammad Shoaib Akhtar

    Hi Genevieve-Brandt-she-her, Thank you for guidance above. I got denoised copy ratio after PostprocessGCNVCaller. Here, I have 2 queries. Please guide.

    1. How I may get denoised ratio of all my samples in one file?

    2. How to interpret absolute copy numbers? I calculated these by multiplying denoised copy ratio with 2. Most of my results are 4. As human genome ploidy is 2 so all those are duplicated?

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    Genevieve Brandt (she/her)

    Hi Muhammad Shoaib Akhtar, for abnormal results, please make a new post with many details so we can look into it and determine what might be the issue.

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