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Old 06-08-2020, 11:40 AM   #1
drdna
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Default 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.
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Old 06-08-2020, 03:09 PM   #2
GenoMax
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Have you marked duplicate reads?
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