SvABA (formerly Snowman) is an SV and indel caller for short-read BAMs. It performs genome-wide local assembly with a vendored SGA, realigns contigs with BWA-MEM, and scores variants by reassembled read support. Tumor/normal, trios, and single-sample modes are supported; variants are emitted as VCF plus a verbose tab-delimited companion (bps.txt.gz) that carries the full per-sample evidence.

• SvABA Main Site

• Module Name: svaba (see the modules page for more information)
• Environment variables set
  • SVABA_HOME
  • SVABA

Allocate an interactive session and run the program.
Sample session (user input in bold):

[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 svaba

[user@cn3144 ~]$ svaba run -t tumor.bam -n normal.bam -G ref.fa -a my_run -p 2 \
          -k chr22 \
          --blacklist tracks/hg38.combined_blacklist.bed 
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load svaba
svaba run -t tumor.bam -n normal.bam -G ref.fa -a my_run -p $SLURM_CPUS_PER_TASK \
          -k chr22 \
          --blacklist tracks/hg38.combined_blacklist.bed

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] svaba.sh

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

svaba run -t tumor1.bam -n normal1.bam -G ref.fa -a run1 -p $SLURM_CPUS_PER_TASK \
          -k chr22 --blacklist tracks/hg38.combined_blacklist.bed
svaba run -t tumor2.bam -n normal2.bam -G ref.fa -a run2 -p $SLURM_CPUS_PER_TASK \
          -k chr22 --blacklist tracks/hg38.combined_blacklist.bed
svaba run -t tumor3.bam -n normal3.bam -G ref.fa -a run3 -p $SLURM_CPUS_PER_TASK \
          -k chr22 --blacklist tracks/hg38.combined_blacklist.bed

Submit this job using the swarm command.

swarm -f svaba.swarm [-g #] [-t #] --module svaba