haplotypes topic
octopus
Bayesian haplotype-based mutation calling
starfish
Intersect multiple VCF files with haplotype awareness
VCF-Simplify
A python parser to simplify and build the VCF (Variant Call Format).
haploclique
Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.
gretel
An algorithm for recovering haplotypes from metagenomes
minorseq
Minor Variant Calling and Phasing Tools
MCHap
Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.
ClairS
ClairS - a deep-learning method for long-read somatic small variant calling
bamsplit
Split a BAM file by haplotype support