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Matt Snyder

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  • markDuplicatesSpark running out of memory

    Answered

    Hi, GATK team and community! I am trying to process a large number of BAM files with MarkDuplicatesSpark run locally (without a spark cluster). These BAM files come from a very deeply sequenced WGS...

  • picard CompareSAMs

    Answered

    Hi! I recently compared BAMs created with two slightly different version of a workflow and used picard CompareSAMs to compare the outputs. In my output tsv all *_DIFFER and MISSING_* are 0 yet ARE_...

  • Insufficient variance error for VariantRecalibrator

    Hi im getting an error trying to test the VariantRecalibrator tool on a human sample.I'm using gatk v4.1.8.1.Here is my command with paths edited for privacy ;) gatk VariantRecalibrator \-R /qual_c...