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choishingwan / PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
http://prsice.info
GNU General Public License v3.0
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it is likely that your base and target data has different encoding for SNPs. You will need to check that. #314

Closed theclairecamp closed 1 year ago

theclairecamp commented 1 year ago 
          it is likely that your base and target data has different encoding for SNPs. You will need to check that.

Originally posted by @choishingwan in https://github.com/choishingwan/PRSice/issues/189#issuecomment-600703938

I actually have this issue, with two different types of encoding for SNPs, my base file is in this format: rs62513865, while my target file is in this format: chr1:54490:G:A

Do you have any recommendations for easily switching the format? I am using build hg19.

choishingwan commented 1 year ago

That's something we tried to implement before I left academic. As of now, the best way to move forward is to update the encoding in your base file to the chr code.