Package: iScanVCFMerge
iScanVCFMergeiScanVCFMerge is a Python tool to facilitate the cross-species application ofIllumina iScan systemmicroarrays. The tool merges VCF genotypes exported fromGenomeStudiowith a second VCF, comprising genotypes derived from other samples and sources. Merging is based on matches of chromosome, position and certain conditions of major and minor alleles, with matched rows from each VCF concatenated into a single row (comprising all individuals) in the output files. The full algorithm is explained in theaccompanying manuscript, where we reported use of the humanInfinium Multi-Ethnic GlobalandInfinium Omni 2.5arrays (hg19) to genotype great apes, and merged those with the genotypes of conspecifics previously published elsewhere.What's new in version 1.1?Bugs fixed to properly handle some multi-allelic sites.The reference population VCF file must now bebgzipped and indexed with tabix. This requirement does not apply to the iScan VCF file, which can either be uncompressed or gzip compressed.In the prior version, the complete reference population VCF file was read into memory before the relevant records were pulled. This caused issues for some users handling enormous reference VCF files. In this version, we use thePysamlibrary's lightweight wrapper of thehtslib C-APIto pull only the relevant records in the first place. The script should now run near-instantaneously, irrespective of input file size.Console output is now handled by the Python logging module and is written to a .log file in the output directory.Version numbering now follows 1.x vs 0.x format for improved compatibility with PyPI.InstallationiScanVCFMerge 1.1 requires Python 3.9. It has been successfully tested on MacOS Big Sur 11.4 and on Ubuntu 21.04.Option 1: Github clone and run with Python3git clone "https://github.com/baneslab/iScanVCFMerge.git"
cd iScanVCFMerge
python3 iScanVCFMerge.pyIf running the script directly with Python, you may also need to install the required packages,e.g.:python3 -m pip install pandas pysamRun Option 2: Install with pippip install iScanVCFMergeorpython3 -m pip install iScanVCFMergeUsageiScanVCFMerge [-h] -I <iScan_vcf> -R <reference_vcf> -O <output_directory>Optional arguments:-h, --help                 Show the help message
-I, --iScanVCF             Path to your iScan VCF file (.vcf or .vcf.gz)
-R, --ReferenceVCF         Path to your reference VCF file, with which the iScan file will be merged. This must be bgzip compressed and be indexed with tabix
-O, --output_directory     Name of the output directory (will be created if it doesn't exist)CitationPlease 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,9:629252, doi: 10.3389/fevo.2021.629252.The (Research Resource Identifier)[https://www.force11.org/group/resource-identification-initiative] for iScanVCFMerge is (RRID:SCR_021193)[https://scicrunch.org/resolver/RRID:SCR_021193].