Mismatch between base and target genotypes causing a "no variants remained" error in PRSice

Question

[arcadian]

There is an error in my PRSice output, where an error occurs saying "no variants remained." The bim file of the base dataset is organised by chromosome:loci whereas the target dataset is by SNP ID. I spoke to my supervisor and he wants me to use awk to change the target base file from SNP ID to match the base dataset one of chromosome:loci. He said that I could use the phenotype file to do so mixed with awk commands. I am quite new to this procedure, hence the challenge. Thanks in advance!

Answer 1

[Sam]

The easiest way will be to change the target dataset's SNP ID to chromosome:loci format unless you are using bgen as your target.

Assuming you have a bim file as your target

awk '{print $1.$1":"$4.$3.$4.$5.$6}' bim > new.bim

(change the file name to appropriate name)