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

SelectVariants Follow

1 comment

  • Avatar
    Georgii Ozhegov

    --remove-unused-alternates don't change the INFO field according to the changes (for example AQ field after removing the unused allele still contains info about this unused allele). Sometimes it can cause errors if downstream analysis includes bcftools.

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk