This is a test version of Biostars. For the public version, visit https://www.biostars.org.
using numeric code for genotype(0= a1a1,2= a2a2 ,3= a1a2 ,4= a2a1) in ped file

dear all

I am new in plink. can I use numeric code for genotype(0= a1a1,2= a2a2 ,3= a1a2 ,4= a2a1) in ped file? and can I use txt or csv files in plink?

thanks a lot

snp
• 1,819 views • link
updated by Biostar Biostar • written by adele adele

Did you read the plink manual?

  1. Why would you want to use those custom genotype codes? Are these standard usage somewhere?
  2. txt is just an extension used to denote "plain text", says nothing of the actual data format. Where do you want to use a csv file in plink? plink take a few inputs, most of which can be generated using plink itself, so where do you want to plug a csv file in?
• 0 views • link
written by Ram Ram

i am reading plink manual. these custom genotype codes are produced from a simulation program and suffixes of the name of files are .txt .
thanks

• 0 views • link
written by adele adele

You can rename the files, and maybe sed the genotype codes?

• 0 views • link
written by Ram Ram

0 answers

No answers yet.

Log in to answer this question.

More posts like this