HVCF is a pilot project to evaluate pros/cons of storing VCF using HDF5 library for web browsing of raw genotype data.
Features:
- Variants are indexed by name (using hash-based index stored on disk) and position (using interval-based index stored on disk).
- Samples are indexed by name (using hash-based index stored on disk).
- Efficient raw level genotype subsetting by position and sample (i.e. row and column) simultaneously.
- Supports compression using GZIP and Blasc LZ4HC.
- Build-in LD (r, r^2) computation using Armadillo linear algebra library.