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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

mapping variant-calling masking
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updated by GenoMax GenoMax • written by Joel Wallenius Joel Wallenius

Technically you can mask it, but what if the variant comes from the pseudogene and not the gene you "want"?

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written by ATpoint ATpoint

Yes, well... surely it's better with some FPs and TPs than nothing at all, eh. Is there another way to do this? Hmm...

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written by Joel Wallenius Joel Wallenius

1 answer

Hey, I found the solution: Use a hg38 reference that does not include alt contigs, e.g.: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.27_GRCh38.p12/GRCh38_major_release_seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

Don't ask me about the 000/001/405 parent folders. I have no idea what they mean. See here for more(?) info: https://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

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written by Joel Wallenius Joel Wallenius

Don't ask me about the 000/001/405 parent folders. I have no idea what they mean.

They are simply parts of the accession number GCA_000 / 001 / 405 used to create a file system hierarchy.

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written by GenoMax GenoMax

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