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

GATK HaplotypeCaller disable filter -DF with the error in positional argument value


1 comment

  • Avatar
    Genevieve Brandt (she/her)

    Frans Dany found the solution for this issue:

    I use the following command:
    $ gatk HaplotypeCaller -R reference-genome-sars-cov-2.fasta -I SRA_final.bam -O SRA.vcf --disable-tool-default-read-filters

    before proceeding with variant filtration step.

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk