Sparse Project VCF: efficient encoding of population genotype matrices.
other · Level V
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- Record sourced from PubMed, PMID 33300997.
- Also identified by DOI 10.1093/bioinformatics/btaa1004 and PMC identifier 8016461.
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Abstract
Variant Call Format (VCF), the prevailing representation for germline genotypes in population sequencing, suffers rapid size growth as larger cohorts are sequenced and more rare variants are discovered. We present Sparse Project VCF (spVCF), an evolution of VCF with judicious entropy reduction and run-length encoding, delivering >10× size reduction for modern studies with practically minimal information loss. spVCF interoperates with VCF efficiently, including tabix-based random access. We demonstrate its effectiveness with the DiscovEHR and UK Biobank whole-exome sequencing cohorts. Apache-licensed reference implementation: github.com/mlin/spVCF. Supplementary data are available at Bioinformatics online.
Medical subject headings
- Genomics
- Software