Dear all,
Could you kindly assist me? I received PED and MAP files (bovine SNP data) from a lab; however, the SNPs were generated using Thermo Fisher's Axiom Bovine Genotyping Chip. I need to perform downstream analyses, mainly comparative analysis using common SNPs from samples genotyped with both Illumina and Axiom platforms.
The SNP IDs differ between the two platforms, so no common SNPs are identified. Could someone with experience working with AXIOM data assist me in converting the AFFY_SNP_IDs to Illumina SNP IDs, or suggest any other method that would enable me to perform analyses such as PCA and ADMIXTURE using one merged file containing common SNPs from samples genotyped on both platforms?
I also have the CEL files for the Axiom Suite.
Thank you in advance for your help!
