bedtools


Introduction:

BEDTOOLS is a collection of tools for carrying out genome arithmetic.

BEDTOOLS can intersect, merge, count, complement, and shuffle genomic
intervals from multiple files. The files may be in a variety of
common genomic formats, including BAM, BED, GFF/GTF, VCF.

The fact that almost all the utilities accept input from stdin
allows one to stream or pipe several commands together to facilitate
more complicated analyses.

Web Site:

The BEDTOOLS home page at github:

https://github.com/arq5x/bedtools2

Reference:

Usage:

On any ARC cluster, check the installation details
by typing "module spider bedtools".

BEDTOOLS requires that the appropriate modules be loaded before it can
be used. One version of the appropriate commands for use on NewRiver is:

module purge
module load gcc/5.2.0
module load bedtools/2.25.0
    

Examples:

The following batch file uses BEDTOOLS to find the base pair overlap
between the CPG and GWAS data:

#! /bin/bash
#
#PBS -l walltime=0:05:00
#PBS -l nodes=1:ppn=1
#PBS -W group_list=newriver
#PBS -q open_q
#PBS -j oe
#
cd $PBS_O_WORKDIR
#
module purge
module load gcc/5.2.0
module load bedtools/2.25.0
#
bedtools intersect -a cpg.bed -b gwas.bed > bedtools_newriver.txt

A complete set of files to carry out a similar process are available in
bedtools_example.tar