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

HaplotypeCaller -ERC GVCF -variant_index_type LINEAR

1

1 comment

  • Avatar
    Bhanu Gandham

    Hi Matilde

     

    You are using a very old version of GATK which we do not support anymore. Please upgrade to the latest version of GATK v 4.1.9.0. The latest version of GATK does not require "-variant_index_type" argument anymore. That was a temporary workaround for an issue with index compression in a very old version of GATK.

    1
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk