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 default 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 core and 1GB of 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