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

VariantRecalibrator Follow


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    Marsha Wallace

    23-Sep-21 'Tutorial' link is broken

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    Zefeng Du

    Dear GATK team,

        It seems that the script provided for VariantRecalibrator has something wrong with the "--resource" augment.

        For example, using

    --resource hapmap,known=false,training=true,truth=true,prior=15.0:hapmap_3.3.hg38.sites.vcf.gz \

        will cause an user error indicating that the file doesn't exist. Instead, it works when I use

    --resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.sites.vcf.gz \

        I think it would be helpful if you fix the tutorial ASAP.

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    Rea Kalampaliki


    Seems like the method documentation, parameters reccomendations and tutorial links link to the main page.

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