PLINK SNP data

Question

[price4890]

Hello,

Can someone please help me? I am not sure what I am doing wrong. I have a a file with SNP data, with each row being a SNP at a particular location of the A. thaliana genome and columns being A. thaliana individuals. Some rows are depicted below. As I understood from reading the manual of plink this is a .tped file. When I run

plink --tped sample_matrix.tped --r2

it gives me

"No file [ plink.tfam ] exists"

How do I create a tfam file from the data given ?

1   snp1     0 73   C   A   A   C   C   A   C   C   C   C   C   C   A   C   C   A   C   C   A   C   A   A   C   A   C   A   A   C   C   C   C   C   C   C   A   C   C   A   C   A   C
1   snp2    0   76  C   C   C   C   C   C   C   C   C   C   C   C   C   C   C   C   C   C   C   C   C   C   C   C   C   T   C   C   C   C   C   C   C   C   C   C   C   C   C   C   C

[Ram]

Please use appropriate tags. Your question is about plink. That should have been a tag when you created the question. When you add appropriate tags, users that follow the tag (usually experts interested in helping others in that subject matter) get notified of your question, and this means you stand a better chance at getting a relevant, useful response faster.

Answer 1

[Fabio Marroni]

tped adn tfam are transposed pedigree and family files. The technical instruction for creating a tfam file are in the plink manual. Follow this link and in the page search for "Transposed filesets".

Basically, as explained in that page: "The TFAM file is just the first six columns of a standard PED file.", so you should be able to create it quite easily. I am not sure if PLINK has an utility for creating it or if you have to do some scripting.

[price4890]

Hi, thanks for the reply

I am just using SNP data from the 1001 Arabidopsis genomes project. So none of the information given by those six columns relates to my data. So that's what I am wondering what to do?