iScanVCFMerge 0.1

Python tool to merge cross-species Illumina iScan genotype data with a reference set of data from a pre-existing source.

iScanVCFMerge

Installation

iScanVCFMerge has been tested with Python 3.9.2 on MacOS Big Sur 11.3 and on Ubuntu 21.04.

Option 1: Github clone and run with Python3

git clone "https://github.com/baneslab/iScanVCFMerge.git"
$ cd iScanVCFMerge
$ python3 iScanVCFMerge.py

If running the script directly with Python, you may also need to install the required packages, e.g.:

python3 -m pip install pandas

Run Option 2: Install with pip

pip install iScanVCFMerge

or

python3 -m pip install iScanVCFMerge

Usage

iScanVCFMerge [-h] -R <reference_vcf> -I <iScan_vcf> -O <output_directory>

Optional arguments:

-h, --help                  Show the help message
-R, --reference_vcf         Reference VCF file against which iScan file will be merged (.vcf or .vcf.gz)
-I, --iScan_vcf             iScan VCF file  (.vcf or .vcf.gz)
-O, --output_directory      Name of the output directory (will be created if it doesn't exist)

Citation

Please cite the use of this software as follows:

Fountain, E. D., Zhou, L-C., Karklus, A., Liu, Q-X., Meyers, J., Fontanilla, I. K., Rafael, E. F., Yu, J-Y., Zhang, Q., Zhu, X-L., Pei, E-L., Yuan, Y-H. and Banes, G. L. (2021). Cross-species application of Illumina iScan microarrays for cost-effective, high-throughput SNP discovery. Frontiers in Ecology and Evolution, doi: 10.3389/fevo.2021.629252.