Specify A Customed Output File For Ld Calculation Using Plink

Question

[J.F.Jiang]

Hi, friends,

Recently I am using PLINK software to calculate the LD among a given SNP set. The software is easy to go while it seems that the LD calculation output file plink.ld can not be self-defined, to deal which must using a script to re-orient the file name.

So is there any other method to obtain a self-defined output ld file?

Thank you for all!

Best!

[dfornika]

Can you clarify what you mean by self-defined output? Do you mean that you want the data to be organized in a different file format? If so, which format? If you have your own custom format, you will likely need to write a perl or awk script to re-format the output.

[J.F.Jiang]

Sorry for confusing. I mean to get a self-defined file name of output for PLINK calculation, not to re-format the output. For example, the output file of LD is plink.ld, I want to get a file named of chr1.snp.ld

Hope I make it clear!

Answer 1

[dfornika]

Take a look at this site for a complete list of command-line options:

http://pngu.mgh.harvard.edu/~purcell/plink/reference.shtml#options

Use the --out flag to change the output filename root. For example, add --out chr1.snp to your command to change plink.ld to chr1.snp.ld

[J.F.Jiang]

Thank you for help