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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

PostprocessGermlineCNVCalls generate a segment file with missing GT field for the segment file

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    Anthony Dias-Ciarla

    Hi NawarDalila,

    Thank you for writing to the GATK forum! I hope that we can help you sort this out.

    The duplications are no-call on purpose because we can't phase them with the tools that we have. So, we don't know if the duplication is one copy on one haplotype and three copies on the other or two copies on each haplotype, which is the information we need to know if we gave it a genotype. So, we don't give it a genotype. Which we recognize is different from SNPs and Indels, which can make some things more complicated, but this is the correct way to represent it.

    Please find more detailed information on using PostprocessGermlineCNVCalls here.

    I hope this helps to clear things up! Please do not hesitate to reach out if you have any other questions.

    Best,
    Anthony

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    Anthony Dias-Ciarla

    Hi NawarDalila,

    We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!

    Kind regards,

    Anthony​

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    Jesús María López Martí

    Hi Anthony Dias-Ciarla,

       regarding the same topic, I have some doubts about how to apply variant filters to DUP genotypes called as './.'. I have tried the tool VariantFiltration (GATK 4.3.0) using different parameters (isNoCall, isCalled,...) to filter those low quality DUP variants. Even I have tried to use inverted filters or the variantContext to keep only the not called genotypes in order to get de DUP variants but everything I have tried ended up ignoring all the DUP variants. On the other hand, the tool SelectVariant  works fine and I am able to keep/filter DUP variants using the same parameters that are not working for VariantFiltration. I have read all the online documentation and I didn't find anything at all. However, maybe I am missing something here. How I should proceed to filter some of the DUP genotypes.

    Best,

    Jesús M

     

     

     

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