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

VCF input example


1 comment

  • Avatar
    Anthony DiCi

    Hi Noam Rudberg,

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

    Firstly, could you please clarify if all t_ref_count and t_alt_count fields are empty?

    For some inputs, the input VCF likely does not have the fields entered in the header (e.g. tumor_sample_barcode). Funcotator allows users to set default annotations for variants that would fill in/annotate some of these fields for you if they weren't already. See argument below.


    For more specifics on Funcotator and its arguments, click here.

    Please let me know about the t_ref_count and t_alt_count fields. Feel free to reach out with any other questions that pop up!


    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk