Question: Mismatch between base and target genotypes causing a "no variants remained" error in PRSice
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gravatar for arcadian
8 weeks ago by
arcadian0
arcadian0 wrote:

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!

bash snp awk linux prsice • 142 views
ADD COMMENTlink modified 8 weeks ago by Sam2.8k • written 8 weeks ago by arcadian0
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gravatar for Sam
8 weeks ago by
Sam2.8k
New York
Sam2.8k wrote:

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)

ADD COMMENTlink written 8 weeks ago by Sam2.8k
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