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

• the read counts across multiple genomes are grouped, normalized, summarized, and graphed in interactive html files
• for an interactive graph example, see this summary and this breakdown for a single chromosome
• a BAM file is a binary sequence alignment map -- see SAMtools for more info
• the read counts and summaries are stored in HDF5 format where they can be efficiently read via Python PyTables or the HDF5 C apis
• the HDF5 files can be viewed directly with the cross platform tool HDFView
• there is an option to output the data in tab delimited text files as well
• there is also a command line utility for counting the number of reads in specified portion of a chromosome, and the count is output to the console

• bamliquidator Main Site

• Module Name: bamliquidator (see the modules page for more information)
• Multithreaded app

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn3144 ~]$ cp -r /usr/local/apps/bamliquidator/test .

[user@cn3144 ~]$ module load bamliqudiator

[user@cn3144 ~]$ bamliquidator_batch test/wgEncodeUwRepliSeqBg02esG1bAlnRep1.bam
Liquidating test/wgEncodeUwRepliSeqBg02esG1bAlnRep1.bam (file 1 of 1)
Liquidation completed: 4.188048 seconds, 1784867 reads, 0.238775 millions of reads per second
Cell Types: test
Normalizing and calculating percentiles for cell type test
Indexing normalized counts
Plotting
-- skipping plotting chrM because not enough bins (only 1)
-- skipping plotting chrM because not enough bins (only 1)
Summarizing
Post liquidation processing took 2.364760 seconds

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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.

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

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 [-g 4] [-t 2] --module bamliquidator