Year: 2024
Type: article
Abstract: Motivation While there are a variety of file formats for storing reference-sequence-aligned genotype data, many are complex or inefficient. Programming language support for such formats is often limited. A file format that is simple to understand and implement – yet fast and small – is helpful for research on highly scalable bioinformatics. Results We present the Indexable Genotype Data (IGD) file format, a simple uncompressed binary format that can be more than 100 times faster and 3.5 times smaller than vcf.gz on Biobank-scale whole-genome sequence data. The implementation for reading and writing IGD in Python is under 350 lines of code, which reflects the simplicity of the format. Availability A C++ library reading and writing IGD, and tooling to convert . vcf.gz files, can be found at https://github.com/aprilweilab/picovcf . A Python library is at https://github.com/aprilweilab/pyigd
Source: Bioinformatics Advances
Authors: Drew DeHaas, Xinzhu Wei
Institution: Cornell University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,917
Awards: G2845033237, G9000136967
OpenAlex ID: W4413637332