Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
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
• 49 views
Read more here: Source link