GenoCore : a simple and fast algorithm for core subset selection from large genotype datasets

The GenoCore python version was developed by Seongmun Jeong and Jae-Yoon Kim.

This program is based on the GenoCore R version available at https://github.com/lovemun/Genocore.

Source code was written in Python language and supported on windows and linux platform.

Usage

1) Download

git clone https://github.com/lovemun/GenoCore_Python

or

git clone https://github.com/JaeYoonKim72/GenoCore_Python

cd GenoCore_Python

2) Basic usage

The GenoCore consists of three submodules: VCFtoCSV, CoreSet, SelectVCF.

Basic usage : python run_genocore.py [ VCFtoCSV | CoreSet | SelectVCF ] [ Options ]

3) VCFtoCSV

The "VCFtoCSV" submodule converts a VCF file into a CSV file for GenoCore. The output file is a CSV file for that VCF.

Usage: python run_genocore.py VCFtoCSV -i [VCF file] -o [Output name] -p [Y or N (phased)] -g [Y or N (gziped)]

Example: python run_genocore.py VCFtoCSV -i ExampleData/Test_420sample.vcf.gz \
                                         -o ExampleData/Test_420sample.csv \
                                         -p Y \
                                         -g Y

4) CoreSet

The "CoreSet" submodule is the main module and performs core sample extraction. The output files are core-sample-list, core-sample-csv and core-sample-coverage files, and removed-marker file.

Usage: python run_genocore.py CoreSet -i [CSV file] -p [Preset txt] -c [Coverage rate] -d [Covergence rate], -o [Output name], -m [MAF]

Example: python run_genocore.py CoreSet -i ExampleData/Test_420sample.csv \
                                        -p ExampleData/Preset.txt \
                                        -c 99 \
                                        -d 0.001 \
                                        -o ExampleData/TestCoreSet \
                                        -m 0.05

5) SelectVCF

The "SelectVCF" submodule extract a core-set VCF file, using the core-sample-list file created by the "CoreSet" module and the input VCF file used by "VCFtoCSV". The output file is a VCF file for final core samples.

Usage: python run_genocore.py SelectVCF -i [VCF file] -g [Y or N (gziped)] -s [Sample list] -o [Output name]

Example: python run_genocore.py SelectVCF -i ExampleData/Test_420sample.vcf.gz \
                                          -g Y \
                                          -s ExampleData/TestCoreSet_CoreSample_list.txt \
                                          -o ExampleData/TestCoreSet_CoreSample.vcf

CoreSet algorithm

The algorithm schematic of "CoreSet", the main submodule, is as follows.

Requirement

The GenoCroe python requires python 3.0 and numpy library. It also works in python 2.0, but python 3.0 is recommended for handling a large data set.

Contact

lovemun@kribb.re.kr

jaeyoonkim72@gmail.com

Citation

Jeong S, Kim JY, Jeong SC, Kang ST, Moon JK, et al. (2017) GenoCore: A simple and fast algorithm for core subset selection from large genotype datasets. PLOS ONE 12(7): e0181420. https://doi.org/10.1371/journal.pone.0181420