Question: Specify A Customed Output File For Ld Calculation Using Plink
1
gravatar for J.F.Jiang
6.5 years ago by
J.F.Jiang750
China
J.F.Jiang750 wrote:

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!

plink ld • 2.3k views
ADD COMMENTlink written 6.5 years ago by J.F.Jiang750

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.

ADD REPLYlink written 6.5 years ago by dfornika1000

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!

ADD REPLYlink written 6.5 years ago by J.F.Jiang750
1
gravatar for dfornika
6.5 years ago by
dfornika1000
Vancouver, British Columbia, Canada
dfornika1000 wrote:

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

ADD COMMENTlink written 6.5 years ago by dfornika1000

Thank you for help

ADD REPLYlink written 6.5 years ago by J.F.Jiang750
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