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

CreateSomaticPanelOfNormals (BETA) Follow


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    Enrico Cocchi

    Hi, I am trying to use your pipeline in gatk 4.1.7 but I saw that the output of passage 2 (GenomicsDBImport) is a folder with some files in it, such as vcfheader.vcf, vidmap.json and what looks like a file for every chromosme with a $ and positions (e.g. X$200786$155255277). But when I try to pass this directory in the -V option of CreateSomaticPanelOfNormals I got an error that is not a regular file, and this documentation states that it is supposed to be a VCF file. So, what is the exact file output from passage 2 that we are supposed to pass here?


    Thank you very much in advance for any help 

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    Brian Wiley

    Under the hood of CreateSomaticPanelOfNormals, does the argument `--min-sample-count` call bcftools isec with --nfiles = to "n" integer passed?

    Actually I looked at code.  Looks like it combines all the counts.  I was thinking it does a sort of bcftools isec to bcftools merge where it keeps samples separate.

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