Converting SNP data table into .traw format or qtl (R) format

Question

[iaagosch]

Hi! I have an excel spreadsheet table with SNP information like the following:

SNP_ID    ind_1    ind_2    ind_3    ind_4    ind_5    ind_6
snp_1     AA       AT       AA       AA       GC       AA
snp_2     TT       AT       TT       TT       TA       TA
snp_3     AA       GC       GG       AA       GG       GG

How can I convert this into a 012 (or AHB) format, being it through plink or R package?

Thank you in advance

Answer 1

[bk11]

Don't you have plink binary (bed/bim/fam) or vcf files? If you do have plink or vcf files, you can do-

#for plink file
plink --bfile plink_data --recode A-transpose --out plink_data_genotypeMatrix
#for vcf file
plink --vcf region.vcf.gz --recode A-transpose --out region_genotypeMatrix

[iaagosch]

Unfortunately, I don’t.

This dataset was given to me in excel format.