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BEDOPS

BEDOPS is a toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.

BEDOPS is available as a module on Apocrita.

Usage

To run the latest installed version of BEDOPS, simply load the bedops module:

module load bedops

For usage documentation, pass the --help switch to any BEDOPS program.

Example job

Serial job

Here is an example job running on 1 cores and 1GB total memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load bedops

# Convert a vcf file to bed format
vcf2bed < test.vcf > test.bed

# Sort the input data
sort-bed test.bed > test_sorted.bed

# Count number of single-base or greated overlaps
bedmap --ec \
       --delim "\t" \
       --bp-ovr 1 \
       --echo \
       --count \
       test_sorted.bed > test_matrix.bed

References