Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.

References:

• B. S. Pedersen and A. R. Quinlan. mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics 2017. PubMed  |  PMC  |  Journal

• mosdepth Main Site: GitHub/mosdepth

• Module Name: mosdepth (see the modules page for more information)
• mosdepth can use multiple threads for bam decompression but does not scale well to more than 4 threads.
• Test data can be found in $MOSDEPTH_TEST_DATA

Allocate an interactive session and follow the example in the following example session.

[user@biowulf]$ sinteractive --mem=10g --cpus-per-task=4 --gres=lscratch:50
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 ~]$ module load mosdepth
[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144 ~]$ cp -rL ${MOSDEPTH_TEST_DATA:-none} data # ~20 GB of data
[user@cn3144 ~]$ # whole exome data analyzed by capture probes
[user@cn3144 ~]$ mosdepth --by data/Agilent_SureSelect_Human_AllExon_V4_Covered.bed \
                      HG00096_WES data/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam

[user@cn3144 ~]$ ls -lh
-rw-r--r-- 1 user group 336K May  8 18:41 HG00096_WES.mosdepth.global.dist.txt
-rw-r--r-- 1 user group 149K May  8 18:41 HG00096_WES.mosdepth.region.dist.txt
-rw-r--r-- 1 user group 570M May  8 18:41 HG00096_WES.per-base.bed.gz
-rw-r--r-- 1 user group  87K May  8 18:41 HG00096_WES.per-base.bed.gz.csi
-rw-r--r-- 1 user group 2.2M May  8 18:41 HG00096_WES.regions.bed.gz
-rw-r--r-- 1 user group 350K May  8 18:41 HG00096_WES.regions.bed.gz.csi

Note that version 0.2.0 produced only a single distribution file ( HG00096_WES.mosdepth.dist.txt.

[user@cn3144 ~]$ # create some graphs. Output file is dist.html
[user@cn3144 ~]$ plot-dist.py HG00096_WES.mosdepth.region.dist.txt

[user@cn3144 ~]$ # WGS data in 500 nt windows. No per-base data is written (-n)
[user@cn3144 ~]$ mosdepth -t3 -n --by 500 HG00096_WGS \
                       data/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam 
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. mosdepth.sh), which uses the input file 'mosdepth.in'. For example:

#! /bin/bash

module load mosdepth/0.3.3 || exit 1

cd /lscratch/$SLURM_JOB_ID || exit 1
mkdir data
cp ${MOSDEPTH_TEST_DATA}/Agilent_SureSelect_Human_AllExon_V4_Covered.bed data
cp ${MOSDEPTH_TEST_DATA}/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam data

mosdepth -n -t2 --by data/Agilent_SureSelect_Human_AllExon_V4_Covered.bed \ 
    HG00096_WES data/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam
plot-dist.py HG00096_WES.mosdepth.region.dist.txt

Submit this job using the Slurm sbatch command.

sbatch --mem=5g mosdepth.sh

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

mosdepth -t2 -n --by 500 sample1 sample1.bam
mosdepth -t2 -n --by 500 sample2 sample2.bam
mosdepth -t2 -n --by 500 sample3 sample3.bam

Submit this job using the swarm command.

swarm -f mosdepth.swarm -g 5 --module mosdepth