Jialab-UCR/Hapi: Inference of Chromosome-length Haplotypes using Genomic Data of Single Gamete Cells

Hapi (short for Haplotyping with imperfect genotype data) is a novel easy-to-use, R package for inference of chromosome-length haplotypes using a few haploid gametes of an individual. The gamete genotype data may be generated from various platforms including genotyping arrays and sequencing even with low-coverage. Hapi simply takes genotype data of known hetSNPs in single gamete cells as input and report the high-resolution haplotypes as well as confidence of each phased hetSNPs. The package also includes a module allowing downstream analyses and visualization of identified crossovers in the gametes.

Getting started

Package details

AuthorRuidong Li, Han Qu, Jinfeng Chen, Shibo Wang, Le Zhang, Julong Wei, Sergio Pietro Ferrante, Mikeal L. Roose, Zhenyu Jia
Bioconductor views Genetics GenomicVariation HiddenMarkovModel Microarray SNP Sequencing SingleCell
MaintainerRuidong Li <rli012@ucr.edu>
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
Jialab-UCR/Hapi documentation built on May 30, 2019, 11:41 a.m.