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

Using the IndexFeatureFile, doesn't recognize -F flag



  • Avatar
    Gijs C

    I don't know why this wasn't included in my post, because I am sure I filled it in. But here is the missing version and command

    REQUIRED for all errors and issues:
    a) GATK version used: v4.2.6.1
    b) Exact command used:  gatk IndexFeatureFile -F clinvar_chr10.vcf

    Comment actions Permalink
  • Avatar
    Anthony DiCi

    Hi Gijs C,

    Thank you for writing to the GATK forum! I hope we can help you sort this out.

    It seems you are referencing an outdated tool index for the IndexFeatureFile command. You are using our most recent version of GATK, Please find the most up-to-date index for this command below.

    IndexFeatureFile - GATK

    You’ll find that -F is no longer used and has updated to -I. Here is the current command.

     gatk IndexFeatureFile \
         -I cohort.vcf.gz

    I hope this helps, please let me know!


    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk