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-   -   GATK calling false SNPs in duplicated regions (http://seqanswers.com/forums/showthread.php?t=94743)

drdna 06-08-2020 11:40 AM

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.

GenoMax 06-08-2020 03:09 PM

Have you marked duplicate reads?


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