Some (hopefully useful) code for GWAS. Predominantly designed to work with the OXSTATGEN suite.

Requirements: python, numpy, scipy

rrm.py

Calculates the realised related matrix on some PLINK binary data. See the methods section of this paper for details:

http://www.nature.com/ng/journal/v42/n7/full/ng.608.html

Usage: python rrm.py [-h] [-snps snps] [-out out] [--ibs out] plinkfile

lmem.py

Performs Genome Wide Association testing using the method described in (for example):

http://www.nature.com/nmeth/journal/v8/n10/full/nmeth.1681.html

usage: python lmem.py [-h] [-genfile genfile] [-header nrows]
           [-covariates covariates] [-weights weights]
           [-linebuffer linebuffer] [--uncorrected uncorrected]
           [-nprocess nprocess] [-jobnum jobnum]
           phenotype kinship output

haps2vcf.py

Converts SHAPEIT2 haplotypes to a phased VCF file.

 usage: python haps2vcf.py [-h] [-output output.vcf.gz] [--flip] input chromo

 positional arguments:
 	    input                 shapeit2 output
   	    chromo                chromosome

 optional arguments:
 	  -h, --help            show this help message and exit
	  -output output.vcf.gz output file
	  --flip                flip alleles