Lumpy detects structural variants from high throughput sequencing data using read-pair, split read, and other signals in parallel.

There are two ways of using lumpy:

• lumpyexpress: Automated and standardized analysis for common situations
• lumpy: Flexible breakpoint detection for more complicated use cases

Either way, lumpy expects input alignments as created by bwa mem.

References:

• Ryan M. Layer, Colby Chiang, Aaron R. Quinlan and Ira M. Hall. LUMPY: a probabilistic framework for structural variant discovery Genome Biol. 2014, 15:R84. Pubmed |  PMC  |  Journal

• lumpy Main Site

• Module Name: lumpy (see the modules page for more information)
• Multithreaded app
• environment variables set
  • $LUMPY_HOME
  • $LUMPY_CONFIG

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 ~]$ module load lumpy

[user@cn3144 ~]$ lumpyexpress -t2 -B /path/to/input.bam
Sourcing executables from
/usr/local/apps/lumpy/0.2.11/bin/lumpyexpress.config ...

Checking for required python modules
(/usr/local/Anaconda/envs/py2.7.9/bin/python)...
samblaster: Version 0.1.22
samblaster: Inputting from stdin
samblaster: Outputting to stdout
samblaster: Opening gcat_set_053.bam.vcf.Kzd6atukx0F1/disc_pipe for write.
samblaster: Opening gcat_set_053.bam.vcf.Kzd6atukx0F1/spl_pipe for write.
samblaster: Loaded 25 header sequence entries.
samblaster: Output 27571 discordant read pairs to gcat_set_053.bam.vcf.Kzd6atukx0F1/disc_pipe
samblaster: Output 0 split reads to gcat_set_053.bam.vcf.Kzd6atukx0F1/spl_pipe
samblaster: Marked 0 of 39432108 (0.00%) read ids as duplicates using 1188k memory in 1M36S(96.300S) C
PU seconds and 19M47S(1187S) wall time.
Removed 5 outliers with isize >= 404
Running LUMPY... 
chrM    1000000
[...snip...]

[user@cn3144 ~]$ lumpyexress -h
usage:   lumpyexpress [options]

options:
     -B FILE  full BAM file(s) (comma separated) (required)
     -S FILE  split reads BAM file(s) (comma separated)
     -D FILE  discordant reads BAM files(s) (comma separated)
     -o FILE  output file [fullBam.bam.vcf]
     -x FILE  BED file to exclude
     -P       output probability curves for each variant
     -m INT   minimum sample weight for a call [4]
     -r FLOAT trim threshold [0]
     -T DIR   temp directory [./output_prefix.XXXXXXXXXXXX]
     -t N     number of threads [1]
     -k       keep temporary files

     -K FILE  path to lumpyexpress.config file
                (default: same directory as lumpyexpress)
     -v       verbose
     -h       show this message

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

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

#!/bin/bash

module load lumpy || exit 1
lumpyexpress -t $SLURM_CPUS_PER_TASK -B input.bam -o output.vcf

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=10 --mem=10G lumpy.sh

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

lumpyexpress -t $SLURM_CPUS_PER_TASK -B input1.bam -o output1.vcf
lumpyexpress -t $SLURM_CPUS_PER_TASK -B input2.bam -o output2.vcf
lumpyexpress -t $SLURM_CPUS_PER_TASK -B input3.bam -o output3.vcf

Submit this job using the swarm command.

swarm -f lumpy.swarm -g 10 -t 10 --module lumpy