README.md

Hapi - Chromosome-length haplotype inference using genotypic data of single gamete cells

Introduction

Hapi is a novel easy-to-use and high-efficient algorithm that only requires 3 to 5 gametes to reconstruct accurate and high-resolution haplotypes 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 the confidence level of each phased hetSNPs. The package also includes a module allowing downstream analyses and visualization of identified crossovers in the gametes.

Manual and R script

The comprehensive manual of Hapi is available here: Hapi Manual. R code of the workflow is available here: Hapi Workflow

Installation

Installation from Github

Hapi can be easily installed from Github by running the following command in R:

### Install dependencies ahead
install.packages('devtools')
install.packages('HMM')

devtools::install_github('Jialab-UCR/Hapi')

If the installation fails with the ERROR: object 'enexprs' is not exported by 'namespace:rlang', please install the developmental version of rlang package first.

devtools::install_github("tidyverse/rlang", build_vignettes = TRUE)

Installation locally

On Windows system

### Install 'HMM' package ahead
install.packages('HMM')

install.packages('Hapi_0.0.1.tar.gz', repos = NULL, type='source')

On Linux and Mac systems

Directly run the following command in R

### Install 'HMM' package ahead
install.packages('HMM')

install.packages('Hapi_0.0.1.tar.gz', repos = NULL, type='source')


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Hapi documentation built on May 2, 2019, 6:52 a.m.