snptools requires Python 3.4+

snptools is a collection of command-line tools written in Python for manipulating high-density genotyping data. To test the tools, run the shell scripts in the test directory. Three file formats are supported: .dsf, .hmp.txt, and .ped. For information on each format, see FORMATS.

Explanations of all options for each tool can be obtained using

$ python3 tool_name.py --help

For tools requiring input/output modes, the following modes are recognized:

1. .dsf
2. .hmp.txt
3. .ped

Use of an undefined mode will generate an error.

$ python3 convert.py -p ../example -i example.hmp.txt -o test.dsf -mi 2 -mo 1

convert converts between different file formats. Be sure that you have specified the correct input and output modes. Specifying the wrong modes will generate undefined behavior.

$ python3 numericalize.py -p ../example -i example.hmp.txt -o test --additive --coding

numericalize converts a file to numeric genotypes, counting minor alleles. The tool also numerically imputes missing genotypes using two times the minor allele frequency (expected value of a binomial random variable).

$ python3 snpstat.py -p ../example -i example.dsf -o example.stat -mi 1

snpstat calculates missing rates and minor allele frequencies for a SNP file. This information is required by filter.