BEDOPS is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.

Documentation

bedops Home Page
bedops Manual

Slurm script

#!/bin/bash
#SBATCH --job-name=bcl2fastq
#SBATCH --time=1:00:00
#SBATCH --partition=norm
#SBATCH --ntasks=1
#SBATCH --mem=64GB
module load bedops
sort-bed GWAS_SNPs.bed > GWAS_SNPs.sorted.bed
bedmap --ec --delim "\t" --bp-ovr 1 --echo --count GWAS_SNPs.sorted.bed LNCaP_DHS.bed > SNP_DHS_matrix.bed