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

Delete <NON_REF> from VCF



  • Avatar
    Tiffany Miller

    Hi ValeriyaVS !

    A symbolic <NON_REF> allele represents non-called but possible non-reference alleles in GVCF files.  If you are running through the best practices, later, the genotyping step will retain only sites that are confidently variant against the reference and these <NON_REF> blocks go away. Follow these steps to do that or run HaplotypeCaller in single sample mode without -ERC GVCF argument. Let me know if this helps!

    Comment actions Permalink
  • Avatar

    Thank you so much! It's work.

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk