Command line arguments#

BALSAMIC#

Balsamic 15.0.1: Bioinformatic Analysis Pipeline for Somatic Mutations in Cancer

BALSAMIC [OPTIONS] COMMAND [ARGS]...

Options

--log-level <log_level>#

Logging level in terms of urgency

Default:

INFO

Options:

NOTSET | DEBUG | INFO | WARNING | ERROR | FATAL | CRITICAL

--version#

Show the version and exit.

config#

Create config files required for running the pipeline.

BALSAMIC config [OPTIONS] COMMAND [ARGS]...

case#

Create a sample config file from input sample data

BALSAMIC config case [OPTIONS]

Options

--analysis-dir <analysis_dir>#

Required Path to store the analysis results

-w, --analysis-workflow <analysis_workflow>#

Balsamic analysis workflow to be executed

Default:

balsamic

Options:

balsamic | balsamic-qc | balsamic-umi

--artefact-snv-observations <artefact_snv_observations>#

VCF path of somatic SNVs called in high coverage normal samples (used in all workflows)

-b, --background-variants <background_variants>#

Background set of valid variants for UMI

--balsamic-cache <balsamic_cache>#

Required Path to BALSAMIC cache

--cache-version <cache_version>#

Cache version to be used for init or analysis. Use ‘develop’ or ‘X.X.X’.

Default:

15.0.1

--cadd-annotations <cadd_annotations>#

Path of CADD annotations

--cancer-germline-snv-observations <cancer_germline_snv_observations>#

VCF path of cancer germline SNV normal observations (WGS analysis workflow)

--cancer-somatic-snv-observations <cancer_somatic_snv_observations>#

VCF path of cancer SNV tumor observations (WGS analysis workflow)

--cancer-somatic-sv-observations <cancer_somatic_sv_observations>#

VCF path of cancer SV observations (WGS analysis workflow)

--case-id <case_id>#

Required Sample ID for reporting, naming the analysis jobs, and analysis path

--clinical-snv-observations <clinical_snv_observations>#

VCF path of clinical SNV observations (WGS analysis workflow)

--clinical-sv-observations <clinical_sv_observations>#

VCF path of clinical SV observations (WGS analysis workflow)

--exome#

Assign exome parameters to TGA workflow

--fastq-path <fastq_path>#

Required Path to directory containing unconcatenated FASTQ files

--gender <gender>#

Sample associated gender

Default:

female

Options:

female | male

-g, --genome-version <genome_version>#

Type and build version of the reference genome

Default:

hg19

Options:

hg19 | hg38 | canfam3

--genome-interval <genome_interval>#

Genome 100 bp interval-file (created with gatk PreprocessIntervals), used for GENS pre-processing.

--gens-coverage-pon <gens_coverage_pon>#

GENS PON file, either male or female (created with gatk CreateReadCountPanelOfNormals), used for GENS pre-processing.

--gnomad-min-af5 <gnomad_min_af5>#

Gnomad VCF filtered to keep >= 0.05 AF, used for GENS pre-processing.

--normal-sample-name <normal_sample_name>#

Normal sample name

-p, --panel-bed <panel_bed>#

Panel bed file of target regions

--pon-cnn <pon_cnn>#

Panel of normal reference (.cnn) for CNVkit

--sentieon-install-dir <sentieon_install_dir>#

Required Path to Sentieon install directory

--sentieon-license <sentieon_license>#

Required Sentieon license in format IP:Port

--swegen-snv <swegen_snv>#

VCF path of Swegen SNV frequency database

--swegen-sv <swegen_sv>#

VCF path of Swegen SV frequency database

--tumor-sample-name <tumor_sample_name>#

Required Tumor sample name

--umi-min-reads <umi_min_reads>#

Minimum raw reads supporting each UMI group. Format: ‘x,y,z’.

pon#

Create a sample config file for PON analysis

BALSAMIC config pon [OPTIONS]

Options

--analysis-dir <analysis_dir>#

Required Path to store the analysis results

--balsamic-cache <balsamic_cache>#

Required Path to BALSAMIC cache

--cache-version <cache_version>#

Cache version to be used for init or analysis. Use ‘develop’ or ‘X.X.X’.

Default:

15.0.1

--case-id <case_id>#

Required Sample ID for reporting, naming the analysis jobs, and analysis path

--fastq-path <fastq_path>#

Required Path to directory containing unconcatenated FASTQ files

-g, --genome-version <genome_version>#

Type and build version of the reference genome

Default:

hg19

Options:

hg19 | hg38 | canfam3

--genome-interval <genome_interval>#

Genome 100 bp interval-file (created with gatk PreprocessIntervals), used for GENS pre-processing.

--sentieon-install-dir <sentieon_install_dir>#

Required Path to Sentieon install directory

--sentieon-license <sentieon_license>#

Required Sentieon license in format IP:Port

-p, --panel-bed <panel_bed>#

Panel bed file of target regions

--pon-workflow <pon_workflow>#

Required Specify which PON to create.

Options:

CNVkit | GENS_male | GENS_female

-v, --version <version>#

Version of the PON file to be generated

init#

Validate inputs and download reference caches and containers.

BALSAMIC init [OPTIONS]

Options

-o, --out-dir <out_dir>#

Required Output directory for singularity containers and reference files

--cache-version <cache_version>#

Cache version to be used for init or analysis. Use ‘develop’ or ‘X.X.X’.

Default:

15.0.1

--account <account>#

Cluster account to run jobs

--cluster-config <cluster_config>#

Cluster configuration JSON file path

--mail-user <mail_user>#

User email to receive notifications from the cluster

--mail-type <mail_type>#

The mail type triggering cluster emails

Options:

ALL | BEGIN | END | FAIL | NONE | REQUEUE | TIME_LIMIT

-p, --profile <profile>#

Cluster profile to submit jobs

Default:

slurm

Options:

slurm

--qos <qos>#

QOS for cluster jobs

Default:

low

Options:

low | normal | high | express

-c, --cosmic-key <cosmic_key>#

Cosmic DB authentication key

--force-all#

Force execution. This is equivalent to Snakemake –forceall.

Default:

False

-g, --genome-version <genome_version>#

Type and build version of the reference genome

Default:

hg19

Options:

hg19 | hg38 | canfam3

-q, --quiet#

Instruct Snakemake to not output any progress or rule information

-r, --run-analysis#

Flag to run the actual analysis

Default:

False

--run-mode <run_mode>#

Run mode to execute Balsamic workflows

Default:

cluster

Options:

cluster | local

-S, --snakefile <snakefile>#

Custom Snakefile for internal testing

--snakemake-opt <snakemake_opt>#

Options to be passed to Snakemake

report#

Command to generate delivery files and check analysis status.

BALSAMIC report [OPTIONS] COMMAND [ARGS]...

deliver#

Report deliver command to generate output analysis files.

BALSAMIC report deliver [OPTIONS]

Options

--disable-variant-caller <disable_variant_caller>#

Run workflow with selected variant caller(s) disable. Use comma to remove multiple variant callers. Valid values are: [‘tnscope_umi’, ‘tnscope’, ‘dnascope’, ‘manta’, ‘cnvkit’, ‘vardict’, ‘merged’, ‘manta_germline’, ‘dellysv’, ‘tiddit’, ‘dellycnv’, ‘ascat’, ‘cnvpytor’, ‘igh_dux4’, ‘svdb’]

-r, --rules-to-deliver <rules_to_deliver>#

Specify the rules to deliver. The delivery mode selected via the –delivery-mode option.

Options:

multiqc | collect_custom_qc_metrics | bam_compress_tumor_umi | bam_compress_normal_umi | bam_compress_tumor | bam_compress_normal | vcfheader_rename_germline | vep_annotate_germlineVAR_tumor | vep_annotate_germlineVAR_normal | modify_tnscope_infofield | modify_tnscope_infofield_umi | gatk_update_vcf_sequence_dictionary | bcftools_filter_tnscope_clinical_tumor_only | bcftools_filter_tnscope_clinical_tumor_normal | bcftools_filter_tnscope_clinical_tumor_only | bcftools_filter_tnscope_clinical_tumor_normal | bcftools_filter_merged_clinical_tumor_only | bcftools_filter_merged_clinical_tumor_normal | sentieon_tnscope_umi | sentieon_tnscope_umi_tn | bcftools_filter_TNscope_umi_clinical_tumor_only | bcftools_filter_TNscope_umi_clinical_tumor_normal | genmod_score_snvs | vep_annotate_somaticSNV_research | svdb_merge_tumor_only | svdb_merge_tumor_normal | bcftools_filter_sv_research | bcftools_filter_sv_clinical | tiddit_sv_tumor_only | tiddit_sv_tumor_normal | delly_cnv_tumor_only | delly_cnv_tumor_normal | ascat_tumor_normal | cnvpytor_tumor_only | vcf2cytosure_convert_tumor_only | vcf2cytosure_convert_tumor_normal | cnvkit_segment_CNV_research | cnvkit_call_CNV_research | vcf2cytosure_convert | finalize_gens_outputfiles | tmb_calculation | msisensorpro_msi_tumor_normal | merge_cnv_pdf_reports

-s, --sample-config <sample_config>#

Required Sample configuration file

status#

Analysis status CLI command.

BALSAMIC report status [OPTIONS]

Options

-p, --print-files#

Print list of analysis files. Otherwise only final count will be printed.

Default:

False

-s, --sample-config <sample_config>#

Required Sample configuration file

-m, --show-only-missing#

Only show missing analysis files.

Default:

False

run#

Run Balsamic analysis on a provided configuration file.

BALSAMIC run [OPTIONS] COMMAND [ARGS]...

analysis#

Run BALSAMIC workflow on the provided sample’s config file.

BALSAMIC run analysis [OPTIONS]

Options

--benchmark#

Profile slurm jobs. Make sure you have slurm profiler enabled in your HPC.

--account <account>#

Cluster account to run jobs

--cluster-config <cluster_config>#

Cluster configuration JSON file path

--mail-user <mail_user>#

User email to receive notifications from the cluster

--mail-type <mail_type>#

The mail type triggering cluster emails

Options:

ALL | BEGIN | END | FAIL | NONE | REQUEUE | TIME_LIMIT

-p, --profile <profile>#

Cluster profile to submit jobs

Default:

slurm

Options:

slurm

--qos <qos>#

QOS for cluster jobs

Default:

low

Options:

low | normal | high | express

--disable-variant-caller <disable_variant_caller>#

Run workflow with selected variant caller(s) disable. Use comma to remove multiple variant callers. Valid values are: [‘tnscope_umi’, ‘tnscope’, ‘dnascope’, ‘manta’, ‘cnvkit’, ‘vardict’, ‘merged’, ‘manta_germline’, ‘dellysv’, ‘tiddit’, ‘dellycnv’, ‘ascat’, ‘cnvpytor’, ‘igh_dux4’, ‘svdb’]

--dragen#

Enable dragen variant caller

--force-all#

Force execution. This is equivalent to Snakemake –forceall.

Default:

False

-q, --quiet#

Instruct Snakemake to not output any progress or rule information

-r, --run-analysis#

Flag to run the actual analysis

Default:

False

--run-mode <run_mode>#

Run mode to execute Balsamic workflows

Default:

cluster

Options:

cluster | local

-s, --sample-config <sample_config>#

Required Sample configuration file

-S, --snakefile <snakefile>#

Custom Snakefile for internal testing

--snakemake-opt <snakemake_opt>#

Options to be passed to Snakemake