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

VariantFiltration filtering all SNPs for all samples to missing



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    Laura Gauthier

    Hi Wiebe Kooistra,

    Given that there is an optional argument `missing-values-evaluate-as-failing` to turn on the behavior of filtering out missing values, no I do not think this is expected behavior.  I'll ask the team to take a look.


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    Wiebe Kooistra

    Hey Laura Gauthier

    Thanks for looking into this :).


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