snptools

Snptools is a tool for SNP (Single Nucleotide Polymorphism) data processing, parentage calculation and call rate estimation.

Introduction

SNP (Single Nucleotide Polymorphism) represent genetic variations, that can be used to analyze genetic data. SNPTools provides a set of tools for working with SNP data, including the following capabilities:

• SNP data processing - FinalReport.
• Parentage Verification and Parentage Discovery Based on SNP Genotypes (ICAR).
• Call rate estimation (percentage of missing data).
• Processing and preparation of data in plink formats.

Installation

You can install snptools via pip from PyPI:

pip install snplib

Usage

Snptools provides commands for a variety of operations. Here are examples of usage:

SNP data processing:

from snplib import FinalReport

Computation of parentage:

from snplib import Discovery, Verification

Preparation format files:

from snplib import (
   Snp, make_fam, make_ped, make_lgen, make_map
)

Stat:

from snplib import (
   hwe, hwe_test, call_rate, allele_freq, minor_allele_freq
)

Documentation

Detailed documentation on how to use SNPTools is available see the docs.

License

This project is licensed under the GNU General Public License - see the LICENSE file for details.