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Short tutorial

Here a short toturial is provided for BALSAMIC (version = 4.2.2).

Step 1. generate a reference -----

Frist reference files must be downloaded. Let's assume BALSAMIC is installed and available at D_BALSAMIC-base_4.2.2, and a COSMIC key is generated via: https://cancer.sanger.ac.uk/cosmic/help/file_download

The following commands will create and download reference directory at ./BALSAMIC_reference (change this path if you want it to be created in another location):

cd BALSAMIC

balsamic config reference \
    --cosmic-key ${COSMIC_KEY} \
    --outdir ./BALSAMIC_reference \
    --singularity BALSAMIC/containers/BALSAMIC_latest.sif

# This might couple of hours
balsamic run reference --configfile reference/config.json --run-analysis

A json file with reference specificaions is created at: BALSAMIC_reference/GRCh37/reference.json

Step 2. Running a test sample -----Now a config file for a test run must be created. Let's use the test data in tests directory:

balsamic config case \
  --tumor tests/test_data/fastq/S1_R_1.fastq.gz \
  --normal tests/test_data/fastq/S2_R_1.fastq.gz \
  --case-id demo_run_balsamic \
  --analysis-dir demo/ \
  --panel-bed tests/test_data/references/panel/panel.bed \
  --reference-config BALSAMIC_reference/GRCh37/reference.json \
  --singularity BALSAMIC/containers/BALSAMIC_latest.sif \
  --output-config demo_run_balsamic.json

Notes:

  • If you want to test tumor_only mode, remove the --normal tests/test_data/fastq/S2_R_1.fastq.gz line.
  • --output-config demo_run_balsamic.json is also optional

Let's try a dry run and see everything is in place:

balsamic run analysis --sample-config demo/demo_run_balsamic/demo_run_balsamic.json

Command above should exit a similar output as below:

Job counts:
count jobs
1 BaseRecalibrator
1 CollectAlignmentSummaryMetrics
1 CollectHsMetrics
1 CollectInsertSizeMetrics
1 IndelRealigner
1 MarkDuplicates
1 RealignerTargetCreator
1 all
1 bwa_mem
1 cnvkit_single
1 fastp
1 fastqc
13  haplotypecaller
1 haplotypecaller_merge
1 manta_germline
1 manta_tumor_only
1 mergeBam_tumor
1 mergeBam_tumor_gatk
1 multiqc
1 mutect2_merge
13  mutect2_tumor_only
1 sambamba_exon_depth
1 sambamba_panel_depth
1 samtools_sort_index
1 somatic_snv_indel_vcf_merge
1 split_bed_by_chrom
1 strelka_germline
1 vardict_merge
13  vardict_tumor_only
7 vep
72
This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.

And now run balsamic through SLURM. Make sure you set your SLURM project account using --account if your local settings require it:

balsamic run analysis --sample-config demo/demo_run_balsamic/demo_run_balsamic.json \
  --profile slurm --qos low --account development --run-analysis

And now run balsamic through QSUB. Make sure you set your QSUB project account using --account if your local settings require it:

balsamic run analysis --sample-config demo/demo_run_balsamic/demo_run_balsamic.json \
  --profile qsub --qos low --account development --run-analysis

And running workflow without submitting jobs. Set number of cores by passing an argument to snakemake as seen below:

balsamic run analysis --sample-config demo/demo_run_balsamic/demo_run_balsamic.json \
  --run-mode local --snakemake-opt "--cores 8" --run-analysis