Human Genome Assembly Converter

Converts chromosome coordinates from one human genome assembly to another

Usage

perl ./human-genome-assembly-converter [-s, -t, -f, -o, --format] CHROM_NAME CHROM_START CHROM_END

Arguments

CHROM_NAME			name of the human chromosome
CHROM_START			starting coordinates	
CHROM_END			ending coordinates

Options

-s,  --source    	source assembly. Default='GRCh37'
-t,  --target      	target assembly. Default='GRCh38'
-f,  --file         input file name which is in BED format
-o,  --output       output file name
-format             Either BED or JSON. Default JSON

Installation

The code has been tested on perl v5.34.0 for x86_64-linux. Before running the script ensure that ensembl perl API has been setup (https://m.ensembl.org/info/docs/api/api\_installation.html). After cloning the repository simply run the command,

$ perl ./human-genome-assembly-converter.pl -s GRCh38 -t GRCh37 10 25000 30000

Currently, it supports output in BED and JSON format. You may also provide an input file in BED format to convert the coordinates.

Tests

The tests directory contains a short script to test the various scenarios.