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bamliquidator

bamliquidator is a set of tools for analyzing the density of short DNA sequence read alignments in the BAM file format

There are multiple versions of bamliquidator available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail bamliquidator

To select a module, type

module load bamliquidator/[ver]

where [ver] is the version of choice.

Environment variables set:

Interactive use

module load bamliqudiator
bamliquidator sorted_and_indexed.bam chr1 0 100000 + 2 200
12345
67890

sbatch

Create a batch input file (e.g. bamliquidator.sh). For example:

#!/bin/bash
module load bamliquidator
bamliquidator_batch.py -n 16 -o test.output directory_of_bam_files/

Submit this job using the Slurm sbatch command, making sure to match the number of threads requested matches the -n option.

sbatch --cpus-per-task=16 --mem=10g bamliquidator.sh

swarm

Create a swarmfile (e.g. bamliquidator.swarm). For example:

bamliquidator sorted_and_indexed.bam chr1 0 1000000 + 2 200
bamliquidator sorted_and_indexed.bam chr1 1000000 2000000 + 2 200
bamliquidator sorted_and_indexed.bam chr1 2000000 3000000 + 2 200
bamliquidator sorted_and_indexed.bam chr1 3000000 4000000 + 2 200

Submit this job using the swarm command.

swarm -f bamliquidator.swarm template.swarm

Examples

Documentation