gwasrecode is a program for extracting and recoding specific markers from PLINK associated .tped-files

It was designed for non programmers

However, one need minimal command line knowledge to use to program properly (see README-FILE)

Functionality and description

• extract specific markers from .tped-files based on:

  • a list of markers saved in a file (each SNP on a separate line)
  • a reference SNP and a definition of bases downstream of the reference SNP - all markers in this range will be extracted

• the .tped files can have common rs-identifier or Illumina exm-identifier (exome data)

  • for the exome-data scenario, a Illumina auxillery file is necessary which contains the annotation from exm- to rs-identifiers

    • Download page for Illumina support files e.g. auxillery files for specific arrays
    • the auxillery file should has two columns: exm-identifier (column 1) and rs-identifer (column 2)
    • the user has to bring the file into the above-mentioned format (if it is not the existing format)

  • the user only has to supply common rs-identifiers, irrespective whether it is exome- or common SNP-chip data

  • gwasrecode was tested under Linux and Windows (version 7 or higher)

• A DETAILED DESCRIPTION OF THE USAGE, ALSO FOR THE GENERAL COMMAND LINE USE, IS WRITTEN IN THE README-FILE

Requirements

Python 2.7.x

Installing

Just download the .zip-file and extract it in a specific folder.

The ReadMe has its own container since there are two pictures which refer to the python installation.

Bugs

Because the program was needed it is not tested for all possible bugs or errors. If you find errors which make no sense or you have a problem in general, please contact me.

Notes

In the near future I want to add extensive comments for the different functions and also to clean the code.

I have to admit that the program is not coded in best coding practice in version 0.35.

Example usage (this is also written in the ReadMe)

Example 1 (based on Windows cmd)

You have exome data and want to extract all SNPs 40000 base pairs down stream of a reference SNP.

Beside -t, -o and -b you have to supply the options -a -s -d -c

• Assume the "test.tped" and "test.tfam" file are stored in the folder "D:\Test\GWAS"
• Assume the auxillery file "data_aux.txt" is stored in the folder "D:\Test\Exomeinfo"
• Assume the reference snp rs1234 on chromosome 2
• Assume we want to extract all SNPs 40000 base pairs down stream of the reference snp
• Assume we only want the recoded models for all extracted SNPs and not the single output file per SNP

The command would be:

python gwasrecode.py -t d:\Test\GWAS\test.tped -o outtest.txt -b no -a d:\Test\Exomeinfo\data_aux.txt -s rs1234 -d 40000 -c 2

Example 2 (based on Windows cmd)

You have common SNP-chip data and want to extract a list of SNPs.

Beside -t, -o and -b you only have to supply the option -l.

• Assume the "test.tped" and "test.tfam" file are stored in the folder "D:\Test\GWAS"
• Assume the SNP-list-file "snps.txt", stored in the folder "D:\Test\GWAS\List" (this file contains rs-numbers you want to extract, every identifier on a new line)
• Assume we want both, the recoded models for all extracted SNPs and the single output file per SNP

The command would be:

python gwasrecode.py -t d:\Test\GWAS\test.tped -o outtest2.txt -b yes -l d:\Test\GWAS\List\snps.txt