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.
The comprehensive manual of Hapi is available here: Hapi Manual.
R code of the workflow is available here: Hapi Workflow
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.
Add R and Rtools to the Path Variable on the Environment Variables panel, including
c:files
c:files-4.6.3
c:files.3.x.x386
c:files.3.x.x64
### Install 'HMM' package ahead
install.packages('HMM')
install.packages('Hapi_0.0.1.tar.gz', repos = NULL, type='source')Directly run the following command in R