liftOverBEDPE

A bash script for converting bedpe files between different genomes builds using NCBI's liftOver tool.

Pre-requisites:

1. liftOver from NCBI has been installed and added to the PATH variable;
2. The liftOver chain file exists (chain files can be downloaded from: https://hgdownload.soe.ucsc.edu/downloads.html)

Usage:

You only need to provide two arguments to the liftOverBEDPE.sh script:

1. input=input.bedpe
2. chain=chain (eg: hg19ToHg38.over.chain)

To invoke liftOverBEDPE.sh, either execute chmod +x liftOverBEDPE.sh first, or type bash liftOverBEDPE.sh input=[input].bedpe chain=[chain] for each liftOver job.