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

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.

To install SNPTools, follow the steps below:

1. Clone the repository into your project directory:

   git clone https://github.com/yourusername/snpTools.git
   

2. Set dependencies:

   pip install -r requirements.txt
   

3. Use SNPTools:

   import snptools
   

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

from snptools.finalreport import FinalReport

from snptools.parentage import Discovery, Verification

from snptools.format import (
   Snp, make_fam, make_ped, make_lgen, make_map
)

from snptools.statistics import (
   hwe, hwe_test, call_rate, allele_freq, minor_allele_freq
)

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

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