Hello, I have some plink data from affymetrix 5.0 arrays and I am converting them to vcfs for imputation. However, I am running into a problem where my vcf files are not matching my reference files. The references I have are the GRch37 fasta and GRch38 primary assembly. Is there a way for me to find out the reference build? am getting 75.5% mismatch when I run bcftools' fixref plugin.
I would advise to use the affy2vcf bcftools plugin to convert the original raw CEL files to VCF rather than trying to convert PLINK data to VCF which is not recommended. Notice that affy2vcf will also allow you to remap the array manifest to GRCh38 or other human genome reference of your choice if you need your genotype data mapped agains the current human genome reference