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

gCNV SVLEN question

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    Anthony Dias-Ciarla

    Thank you for your post, Adriana ! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

    Please see our Support Policy for more details about how we prioritize responding to questions. 

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    Laura Gauthier

    Hi Adriana!

    It looks like I was the one who added those to the GCNV segments VCF header.  :-)  PostprocessGermlineCNVCalls also gets used in the GCNV joint calling pipeline, which is where those annotations actually have informative values.  (They get added by the JointGermlineCNVSegmentation tool.)  So, no, you shouldn't expect those annotations to show up if you're just running on a single sample.  I'll see if there's a way I can limit the header output to just the multi-sample model to avoid confusion in the future.  I'm glad to see GCNV is getting some use outside the Broad!

    Best,

    Laura

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    Laura Gauthier

    P.S. I think you change those Ns to the actual reference base at that position if you supply a reference fasta with the -R argument.  N is showing up in the REF column of the VCF and I expect the INFO field to have just "END"s.

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    Anthony Dias-Ciarla

    Hi Adriana,

    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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