Creation Of Plink Files

Question

[nikospsa]

Hello

I am trying to create the ped file for plink and i have some questions

First of all i used the affymetrix console for genotyping. I just have the .cel files so i can't export plink files from the affymetrix console cause i dont have the .arr files i need. After the genotyping in the summary snp table i have 900k+ snp. About 7000 of them dont have the dbSNP RS ID that plink needs so i deleted them from my list.

Now for the .ped file for the marker columns i can get only call codes after the genotyping with the birdseed algorithm (AA AB BB) for each snp.

My first question is will this be a problem for plink if i use the call codes for markers? Now in the files with the call codes i have all the snp including those i erased because of the lack of dbSNP RS ID and its really difficult to find them and delete them in all my files (51 in count). So i guess this will be a problem for plink cause it wont be able to match the markers with the snp in the map file?! Any suggestions on this?

And finally is there any way (script or anything else) that can get the call codes from the 51 files transpose them (because the callcodes are in column and i want them in row) and put them all in one file?

thank you in advance

Answer 1

[zx8754]

SNP names doesn't have to start with rs they can be named anything, no need to drop. Yes, it can be coded as AA, AB, BB, plink doesn't mind as long as it is a combination of only 2 letters - A and B. However, we need to use --missing-genotype to indicate which character is used. There is a relevant question here.