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

Funconator's ignore-filtered-variants is not a recognized option

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    Pamela Bretscher

    Hi Stephen Chung,

    I do see that --ignore-filtered-variants is listed in the tutorial documentation for Funcotator. However, this option is not listed in the Funcotator Tool Documentation. The tool documentation lists the --remove-filtered-variants option which I believe should accomplish the same thing. I am not sure why there is a discrepancy in what is listed in the tutorial and tool documentation, but could you try using --remove-filtered-variants instead and let me know if this works?

    Kind regards,
    Pamela

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