An installation helper, perl wrapper and the R program Battenberg which detects subclonality and copy number in matched NGS data.

• cgpBattenberg GitHub repo

• Module Name: cgpBattenberg (see the modules page for more information)
• cgpBattenberg.pl can use multiple threads (-t). Please match the number of threads with
• cgpBattenberg is part of the Cancer Genome Project and is closely related to the programs BRASS and Ascat NGS as well as the utilites VAGrENT and PCAP-core. All of these programs can be added to your path using the cancerit-wgs module. To get the most recent versions of all of these, use the cancerit-wgs/latest module version. the number of allocated CPUs
• Reference data in /fdb/cancerit-wgs/cgpBattenberg/

Allocate an interactive session and run the program. Sample session. Note that the cgpBattenberg.pl is part of the cancerit-wgs tools.

[user@biowulf]$ sinteractive --cpus-per-task=4
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 cgpBattenberg
Usage:
    battenberg.pl [options]

      Required parameters:
        -outdir                -o   Folder to output result to.
        -reference             -r   Path to reference genome index file *.fai
        -tumbam                -tb  Path to tumour bam file
                                     - when '-a' defined sample name
        -normbam               -nb  Path to normal bam file
                                     - when '-a' defined sample name
        -gender                -ge  Gender, XX, XY or L (see -gl)
        -impute-info           -e   Location of the impute info file
        -thousand-genomes-loc  -u   Location of the directory containing 1k genomes data
        -ignore-contigs-file   -ig  File containing contigs to ignore
                                    - specifically male sex chromosome, mitochondria and non primary contigs
        -gc-correction-loc     -gc  Path to gc correction files

      Optional parameters:
[...snip...]

[user@cn3144]$ battenberg.pl -p output \
    -r /fdb/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa \
    -tb tumor.bam \
    -nb normal.bam \
    -ge XX \
    -impute-info /fdb/cancerit-wgs/cgpBattenberg/impute/impute_info.txt \
    -thousand-genomes-loc /fdb/cancerit-wgs/cgpBattenberg/1000genomesloci \
    -ignore-contigs-file ignore_contigs \
    -gc-correction-loc /fdb/cancerit-wgs/cgpBattenberg/battenberg_wgs_gc_correction_1000g_v3 \
    -species Human -assembly 37 \
    -t $SLURM_CPUS_PER_TASK


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

Notes:

• The ignore contigs file should include the Y, MT, and non-primary contigs. Running without this will result in errors.
• Increasing the number of threads results in a proportional increase in the amount of memory required. In one test I was able to run 6 threads with 40GB of memory with tumor and normal files of approximately 25GB.

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

#!/bin/bash
module load cgpBattenberg
battenberg.pl -p output \
    -r /fdb/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa \
    -tb tumor.bam \
    -nb normal.bam \
    -ge XX \
    -impute-info /fdb/cancerit-wgs/cgpBattenberg/impute/impute_info.txt \
    -thousand-genomes-loc /fdb/cancerit-wgs/cgpBattenberg/1000genomesloci \
    -ignore-contigs-file ignore_contigs \
    -gc-correction-loc /fdb/cancerit-wgs/cgpBattenberg/battenberg_wgs_gc_correction_1000g_v3 \
    -species Human -assembly 37 \
    -t $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=16 --mem=30g cgpBattenberg.sh

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

battenberg.pl -p output -tb tumor1.bam -nb normal1.bam ... -t $SLURM_CPUS_PER_TASK 
battenberg.pl -p output -tb tumor2.bam -nb normal2.bam ... -t $SLURM_CPUS_PER_TASK 
battenberg.pl -p output -tb tumor3.bam -nb normal3.bam ... -t $SLURM_CPUS_PER_TASK 

Submit this job using the swarm command.

swarm -f cgpBattenberg.swarm -g 30 -t 16 --module cgpBattenberg