CHR is all NA error

[Shinya Tasaki]

Hello, 

I've experimented with PENNPRS and encountered the following error when using the attached input. The input contains CHR values without any missing data, so I'm not sure why I'm receiving this error. I appreciate your help.

Best,

Shinya

################## PennPRS version 1.0.0 ##################

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##################### Loading Data ########################
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Processing file: TRAIT_Alzheimer.s.disease__Author_Bellenguez.C__Journal_Nat.Genet__Year_2022__ACC_GCST90027158 (2).txt.gz
Unzipping gzipped file.
Column configuration is correct.
Column CHR is all NA
Column with all NA values: CHR
Stopping the script.

[Jin Jin]

Dear Shinya,

Thank you for reaching out to us regarding the issue you encountered! The issue with the data is the format for the SNP column - in your data, the format for the SNP column is "chr6:32361867:C:T", but we only allow RSID, which will be used to match the input GWAS data with our reference genotype data. In your case, if you do not have the RSID information in your current dataset, I suggest using the 1000 Genomes reference data (GRCg38) to impute the RSID based on CHR and position information. To avoid confusion, we will update our website with a more specific instruction on the required format for the SNP column. Please let us know if you have further questions.

Thanks!

PennPRS Team

[Shinya Tasaki]

This is good to know. Thank you for your prompt assistance!