This repository has been merged with happyR, and will no longer be updated.
happyCompary offers a set of functions to facilitate downstream analysis of variant calling performance outputs from hap.py. It builds on top of happyR to support annotation of hap.py results (e.g. grouping) through metadata samplesheets, and provides methods for quick retrieval, statistical analysis and easy reporting of performance metrics.
devtools::install_github("Illumina/happyCompare")Read the Quick start guide for summarised instructions on how to load data from happyCompare samplesheets, access metrics and visualise results.
Development and testing for happyCompare have been done using R 3.3.3 on a Centos 6.9 machine, with 2 processor cores and 8GB of RAM. Alternative systems are also supported as documented in the official R installation guide.