Hello friends,

How to compare the genotype calls of the SNPs on chromosome X for the GWAS samples between the GWAS Plink file and the Affymetrix genotype output file to confirm whether the chromosome X genotype calls are 100% identical in the two files?

He provided me sample sheet (sample-well position, sampleID, status, batch, Gender, Age), MAP file(Chromosome, MarkerID, Genetic Distance, Physical position) and PED file (FamilyID, SampleID, PaternalID, MaternalID, Sex, Affection, Genotype). Is the Affymetrix genotype output files refer to "CEL and ARR" files?

I am just trying to help one of my technicians. I don't have much background on plink files and affymetrix output files.