Fast and simple haplotype counting.

Haplotype Fixation Index for crop populations with homozygous nature, such as rice

Haplo- and Diplotype Star Allele matcher for Drug Dosage Guidelines

The bash script reformats SHAPEIT .haps file to show samples by rows instead of variants by rows

A set of functions for filtering erroneous sequences in eDNA metabarcoding data

PBWT-based algorithm for identifying all Maximal Perfect Haplotype Blocks with Wildcards

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

TFM_AliciaAranda_QApckg

a C++ program for haplotype reconstruction using HMM

Calculate SMD and Hamming and Jaccard distances between each pair of samples in a set of variant files.

Chromosome Overlap: code accompanying "Refining the genetic risk of breast cancer with rare haplotypes and pattern-mining" by Letsou et al. DOI: 10.26508/lsa.202302183

A data and code repository for the paper of the same name.

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

Scripts to automate the phasing with several tools

Docs for AmpliPiper, developed by @nhmvienna

A novel bioinformatics tool in Java to build phased long alleles of STR+SNP+InDel from VCF file

A pipeline for phasing haploptypes using short readbackphased haplotype blocks in population of samples.

Construct gene haplotype with VCF format files and snpEff annotation.

This is a tutorial that shows how phaseExtender can be used for recursive improvement of haplotype phasing and how to test the phasing quality by measuring switcherrors.

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