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
Download the package Hapi_0.0.1.tar.gz
Make sure you have Rtools installed
Add R and Rtools to the Path Variable on the Environment Variables panel, including
c:\program files\Rtools\bin
c:\program files\Rtools\gcc-4.6.3\bin
c:\program files\R\R.3.x.x\bin\i386
c:\program files\R\R.3.x.x\bin\x64
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')
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')