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  • #1

    GATK snp calling

    The number of LowQual using ApplyRecalibration as the same as the LowQual in raw.vcf.
    LowQual number does not change!!! and a little PASS change to TruthSensitivityTranche99.00to99.90.
    should I filtering itself based on the VQSLOD values? I followed the pipeline:
    Page not found
    http://www.broadinstitute.org/gsa/wi...th_the_GATK_v3
    If you are unable to find something or have a question about our new website, please email [email protected]. For other inquiries related to the Broad Institute, the necessary contact information can be found here.
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