Simple and portable approach for recalibration and variant calling on non-human data

(*) Overview This repository provides genomic resources for genetic variant discovery. Utilizing the GATK pipeline, we offer a standardized, modular, and fully reproducible framework that transforms raw Next-Generation Sequencing (NGS) data into high-quality Variant Call Format (VCF) datasets. Our goal is to facilitate genomic research and promote the principles of open data sharing. For each species, the repository includes: ✔ pseudoDB: A simulated database of genetic variants. ✔ dbSNP_variant_calling: A collection of variants identified using the established dbSNP database. ✔ pseudoDB_variant_calling: A collection of variants identified utilizing the newly generated pseudoDB. (*) List of species and their databases : DOI(10.5281/zenodo.fileID) Species PseudoDB Identified variants Human 7488070 7489312 Rice 7488383 7489188 Sheep 7488425 7489263 Chickpea 7487929 7489377 African oil palm 18437285 18344327 Brown bear 18437343 18349717 Komodo dragon 18437361 18349005 Stevia 18437378 18347147 Swan goose 18437393 18348479 Cattle 18333082 18350358 (*) Contact For further information regarding the analytical methods, results, or reproducibility, please contact Dr. Sunhee Kim (king@kongju.ac.kr) at Kongju National University, Korea, or HyeonJung Lee (hyeon@kaist.ac.kr) at the Korea Advanced Institute of Science and Technology (KAIST).