ClairS - a deep-learning method for long-read somatic small variant calling

A python parser to simplify and build the VCF (Variant Call Format).

An algorithm for recovering haplotypes from metagenomes

Intersect multiple VCF files with haplotype awareness

Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.

Split a BAM file by haplotype support

A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.

Tools for data conversion and results visualization for fineRADstructure (http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html)

Long sequencing reads classifier

Proteogenomics database-generation tool for protein haplotypes and variants

Collection of several small tools. These tools stay here temporarily and may move to other major repositories as they evolve.

SNP pipeline using Snakemake for the Weisrock Lab's Tiger Salamander project.

Scripts to automate the phasing with several tools

Haplo- and Diplotype Star Allele matcher for Drug Dosage Guidelines

This program leverages zero recombination clusters and their relative positions on a linkage group to impute phases for missing data with high fidelity.