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

Funcotator: VCF output

0

2 comments

  • Avatar
    Bhanu Gandham

    Hi TMB

     

    You don't need to create separate VCF files - you can run both gnomad versions on the same VCF at the same time by enabling the gnomad data sources (unzipping the included gnomad tar.gz files). This will cause GATK to reach out to the internet and read the gnomad data source with NIO and will cause funcotator to perform more slowly.The resulting annotated variants will be labeled with both gnomAD_exome and gnomAD_genome. This is the only practical way to include the gnomad datasource
    0
    Comment actions Permalink
  • Avatar
    TMB

    Thank you for clarifying!

    TMB

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk