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

CollectFragmentCounts (BETA) Follow


  • Avatar
    Subinoy Biswas

    I am using gatk conda package and I got the following error

    "A USER ERROR has occurred: 'CollectFragmentCounts' is not a valid command."

    Please tell what's the equivalent command in the gatk version.



    Comment actions Permalink
  • Avatar
    Fong Chun Chan

    According to, it seems to have now been replaced with CollectReadCounts.

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk