Usage

SNAPPY was recently moved to a package installation rather than a standalone script. Some details recorded below may not be applicable to the package installation.

Quick Start:

Download or clone SNAPPY, then navigate in the terminal to the folder where SNAPPY is saved. The folder should also contain the files parse_ref_files.py, parse_plink_files.py, and a directory called ‘ref_files’ that contains four additional files. Run SNAPPY with the following command:

snappy --infile plink_library

where plink_library is the prefix name of the genotypes to be analyzed. Note that SNAPPY uses plink (v1.9) in a preprocessing step so a plink (v1.9) executable must be listed in the user’s path as plink for preprocessing steps. If plink (v1.9) is not available in the path, the input can be created manually using plink (v1.9) with the –recodeAD option. plink is available for all major operating systems and can be downloaded here.

Installation:

Download or clone SNAPPY, then navigate in the roo of the the local SNAPPY repository in terminal. Run the following commands:

python setup.py sdist
pip install dist/snappy-X.X.tar.gz

SNAPPY is now installed as a command-line tool and can be accessed from any directory. To test the installation, navigate to the root of the local SNAPPY repository, then run:

snappy --infile test_data/TGP_chrY --out test_SNAPPY

Test SNAPPY’s output against the output distributed with the software:

diff test_SNAPPY.all test_data/TGP_SNAPPY_results.all > test_SNAPPY_diffs.txt

A working installation of SNAPPY should yield an empty file test_SNAPPY_diffs.txt.