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  • GATK calling false SNPs in duplicated regions

    Is there a way to prevent GATK from calling SNPs in regions containing sequences that are duplicated in the reference genome? I'm having a problem with it calling false SNPs based on alignments of multi-mapped reads.

    Tried running GenotypeGVCFs with the --read-filter NotSecondaryAlignmentReadFilter flag but this made no difference.

  • #2
    Have you marked duplicate reads?

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