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
Technically you can mask it, but what if the variant comes from the pseudogene and not the gene you "want"?
Yes, well... surely it's better with some FPs and TPs than nothing at all, eh. Is there another way to do this? Hmm...