plink scoring output for multiple files
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2.4 years ago
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Hi all, I am using plink to create a profile score for multiple genes present in aorta tissue. I wrote the names of the input files for the plink command in the separate file and wrote a simple script which loops in the input files and run the plink command on it. The code is as follows: for FileName in $(cat testFileNames.txt); do plink --bfile 1000G_20101123_v3_281K_bestguess_thres0_chr1_X_280311_1586_1142_797_Populationcontrols --score $FileName 1 2 4; done

But the above code is generating the scoring profile named "plink.profile" only for the last file, whose name is present in the testFileNames.txt. For example, the testFileNames.txt contains


The above command would generate only a single .profile file listing the values for the Artery_Aorta.ENSG00000000971.11.wgt.RDat.txt gene. I would have expected the command to generate a separate .profile output files for each of the input file. Is there some way around for it as I need to generate the scores for 6000 genes?


SNP genome plink allele scoring • 639 views

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