Strelka is an analysis package designed to detect somatic SNVs and small indels from the aligned sequencing reads of matched tumor-normal samples.

References:

• Saunders et al.Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs. Bioinformatics (2015). Link

• Strelka Main Site

• Module Name: strelka (see the modules page for more information)
• Multithreaded app
• environment variables set
  • $STRELKA_INSTALL_DIR
• Example files in $STRELKA_TEST_DATA

Running strelka is a two step process:

1. Configure the workflow with configureStrelkaWorkflow.pl. Example configuration files for this step can be found in $STRELKA_INSTALL_DIR/etc.
2. Run the makefile generated in step 1

The current version still does not support parallelization across more than one node (i.e. the workflow engine used does not support submitting tasks as jobs with SLURM).

Illumina recommends first running manta on the samples and supplying manta's candidate indels as input to strelka with the --indelCandidates command line option. The example below skips this step.

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

[user@biowulf]$ sinteractive --cpus-per-task=10 --mem=10g
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 strelka/2.7.1

[user@cn3144 ~]$ cp -r $STRELKA_TEST_DATA/demo . # copy example data

[user@cn3144 ~]$ cd demo

[user@cn3144 ~]$ # configure the workflow with 'configureStrelka${type}Workflow.py'
                 # where type is Starling, Germline, or Somatic

[user@cn3144 ~]$ configureStrelkaSomaticWorkflow.py \
              --normalBam=data/NA12892_dupmark_chr20_region.bam \
              --tumorBam=data/NA12891_dupmark_chr20_region.bam \
              --referenceFasta=data/chr20_860k_only.fa \
              --runDir demo_out

[user@cn3144 ~]$ demo_out/runWorkflow.py -m local -j $SLURM_CPUS_PER_TASK

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

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

#!/bin/bash
module load strelka/1.0.15 || exit 1

configureStrelkaSomaticWorkflow.py \
  --normalBam=/path/to/normal.bam \
  --tumorBam=/path/to/tumor.bam \
  --referenceFasta=/path/to/hg19.fa \
  --runDir=/path/to/myAnalysis

# -j N allows make to use up to N parallel processes

demo_out/runWorkflow.py -m local -j $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=24 --mem=100g strelka.sh

Several things must be changed in this script:

• /path/to/normal.bam : Alignment (BAM) file for normal reads
• /path/to/tumor.bam : Alignment (BAM) file for tumor reads
• /path/to/hg19.fa : Reference (FASTA) file for the alignment
• /path/to/myAnalysis : Output directory

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

demo_out1/runWorkflow.py -m local -j $SLURM_CPUS_PER_TASK
demo_out2/runWorkflow.py -m local -j $SLURM_CPUS_PER_TASK
demo_out3/runWorkflow.py -m local -j $SLURM_CPUS_PER_TASK

Submit this job using the swarm command.

swarm -f strelka.swarm -g 100 -t 24 --module strelka