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Enrico Cocchi

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  • Mutect2 PoN - GenomicsDBImport creates empty DB

    Answered

    I am trying to follow GATK 4.2.0 best-practice guidelines for Mutect2 PoN creation. I called variants in my samples as recommended with: gatk Mutect2 \-R ${REF} \-L ${EXOME_INPUT_INTERVALS} \-I ${...

  • GATK Mutect2 tumor vs. normal sample

    Answered

    a) How do I compared somatic variants called through a PoN file with the latest best-practive-guidelines between a normal-sample and a tumor-sample in order to know which one are characteristics of...

  • Mutect2 missing variant

    Hi, I am using GATK 4.1.2.0 and I noticed a strange behavior by Mutect2. The variant 13-33329989-TGTCTC-T is called if the BED file contains: 13 33329959 33330170 but not if it contains: 13 3...