ID naming#
TOPMED returns chr:pos:ref:alt.
rsid
REF:ALT to major:minor translation#
if (AF == MAF) => ALT = minor, REF = major
SNP matching#
switching#
flipping#
SNP: chr:pos:alt:ref
How do I know if it matches chr:pos:allele_1:allele_2
- First:
chr:posare equivalent - Second: Matching four scenarios
If it matches, use the target variant id (often the variant in the plink files) as the new id.