Filtering vcf with dbSNP
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Entering edit mode
8 months ago
whb ▴ 20

Hi,

From NCBI website, dbSNP accepts both disease or not SNPs https://www.ncbi.nlm.nih.gov/books/NBK44447/#Content.what_classes_of_genetic_variatio.

I have some samples that do not have matching normals. I have done it with Mutect2 but want to use another caller to further verify my findings. My plan is to variant call using tumour-only mode and then filter it with dbSNP using bcftools isec.

My question is will I be filtering out some disease SNPs (e.g. p53 etc) that are important for my study? is there any way to distinguish the disease SNPs in the dbSNP to make sure they won't get filtered out?

Thank you!

dbSNP filter bcftools • 304 views
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