Question: Mismatch between base and target genotypes causing a "no variants remained" error in PRSice
0
gravatar for arcadian
9 months 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 • 576 views
ADD COMMENTlink modified 9 months ago by Sam3.3k • written 9 months ago by arcadian0
0
gravatar for Sam
9 months ago by
Sam3.3k
New York
Sam3.3k 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 9 months ago by Sam3.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2570 users visited in the last hour
_