I used TOPMED imputation server to impute my genotype data, and I observed some variants with alleles that consist of more than one nucleotide/base. I am unsure how to interpret such allele information. Could these be artifacts from the imputation process, or true multi-allelic sites?
For example, below is the variant ID and genotype information for a SNP that was imputed on TOPMED. The alternative allele for this SNP is known to be 'A' according to reference databases, but its genotypes were 'GT' and 'G' in the TOPMED output. I have also extracted this SNP from the same dataset imputed via the Michigan Imputation server and an independent cohort imputed via TOPMED, and observed the same allele information.
Header for SNP in .vcf file (TOPMED output):
chr4 83320925 chr4:83320925:G:GT G GT . PASS AF=0.12128;MAF=0.12128;R2=0.9538;IMPUTED GT:DS:HDS:GP
SNP in .bim file (converted from the above .vcf file):
4 rs1434276157 0 83320925 GT G
Corresponding rsID and genotype info in SNP151 reference file
1220 chr4 83320925 rs1434276157 + G G A/G genomic
Before and after updating variant ID to rsID in .bim file:
4 chr4:83320925:G:GT 0 83320925 GT G
4 rs1434276157 0 83320925 GT G
Thank you!
