Skip to content

jaredo/gwas

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

11 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

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

About

Some useful code for GWAS

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages