Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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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

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    Anthony Dias-Ciarla

    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.

    --annotation-default

    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!

    Best,
    Anthony

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