Upstream pseudogene causing MAPQ 0 and exclusion during variant calling

Upstream pseudogene causing MAPQ 0 and exclusion during variant calling

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Hello,

just upstream of GBA1 is a pseudogene that is quite similar to GBA1, this makes most of my mapped reads have MAPQ 0 across this region (I think? I use bwa-mem2 with default settings), and the variants are not listed in the corresponding VCF file.

Can I remedy this somehow? Mask the pseudogene and map again?

Sincerely,
Joel


Mapping


Variant-calling


masking

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