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

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!

prsice snp linux bash awk

1 answer

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)

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