Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

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

1 comment

  • Avatar
    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 

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk