I am trying to convert from .ped and .map files (output from PLINK) to some sort of gene-dosage format for use in an eQTL study (0 = homozygous minor, 1 = heterozygote, 2 = homozygous major.)
I tried coding this up myself, but ran into a problem when I discovered that I have no way of knowing which allele is major and which is minor. I have legend files listing "allele1" and "allele2", but by looking at dbSNP I discovered that there is no correlation between allele1/2 and major/minor.
I did see this answer : Conversion of ped/map or bim/bim/ fam files to dosage for GWAs mit Probable and comparison with imputated genotypes but I was not able to use genABEL because I don't know what an "infofile" is. (yes, I saw the answer someone posted to my question, but it didn't tell me what an "infofile" is.)
I tried using fcgene (http://sourceforge.net/projects/fcgene/) which claims to convert to dosage format, but this only gave me a list of SNPs as output!
Someone has to have written a ped->dosage conversion tool already, but I can't seem to find it. Could someone point me in the right direction?