Command line arguments

BALSAMIC

Balsamic 19.0.0: 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

Configure BALSAMIC workflow based on input arguments.

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)

--artefact-sv-observations <artefact_sv_observations>

VCF path of somatic SVs called in high coverage wgs normal samples used in WGS

-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:

19.0.0

--cadd-annotations <cadd_annotations>

Path of CADD annotations

--cancer-genelist <cancer_genelist>

Tab-delimited file with cancer-genes downloaded from OncoKB

--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-snv-panel-observations <cancer_somatic_snv_panel_observations>

VCF path of cancer SNV tumor observations from matching gene panel

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

VCF path of cancer SV observations (WGS analysis workflow)

-c, --cosmic <cosmic>

Required Cosmic VCF path

--case-id <case_id>

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

--cust-case-id <cust_case_id>

Case ID from customer

--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)

--soft-filter-normal

Flag to disable hard-filtering on presence of variants in matched normal sample

--exome

Assign exome parameters to TGA workflow

--fastq-path <fastq_path>

Required Path to directory containing unconcatenated FASTQ files

--gender <gender>

Case associated Gender

Default:

unknown

Options:

female | male | unknown

-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’.

--rescue-snvs <rescue_snvs>

Path to rescue file for SNVs, see read-the-docs for format.

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:

19.0.0

--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

--workflow-partition <workflow_partition>

Cluster node partition to run Snakemake jobs

Default:

core

--headjob-partition <headjob_partition>

Cluster node partition to run Snakemake head-job

--cache-version <cache_version>

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

Default:

19.0.0

--account <account>

Cluster account to run jobs

--max-run-hours <max_run_hours>

The maximum number of hours that the sbatch script for snakemake is allowed to run on the cluster.

Default:

168

--cache-profile <cache_profile>

Directory containing snakemake cache profile specifying rule resources for cache workflow

Default:

/home/docs/checkouts/readthedocs.org/user_builds/balsamic/checkouts/stable/BALSAMIC/constants/cache_profile

--qos <qos>

QOS for cluster jobs

Default:

low

Options:

low | normal | high | express

--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

--run-interactively

Run Snakemake job submission interactively instead of submitting the submitter to cluster.

-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

-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 | sentieon_tnscope_umi | sentieon_tnscope_umi_tn | sentieon_tnscope_tga_tumor_normal | sentieon_tnscope_tga_tumor_only | sentieon_tnscope_wgs_tumor_only | sentieon_tnscope_wgs_tumor_normal | vardict_move_svs | 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 | 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_normal_wgs | tiddit_sv_tumor_only_wgs | delly_cnv_tumor_only | delly_cnv_tumor_normal | delly_cnv_tumor_normal_wgs | delly_cnv_tumor_only_wgs | ascat_tumor_normal_wgs | cnvpytor_tumor_only_wgs | 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 | create_cnv_html_report

-s, --sample-config <sample_config>

Required Sample configuration file

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

--workflow-partition <workflow_partition>

Cluster node partition to run Snakemake jobs

Default:

core

--headjob-partition <headjob_partition>

Cluster node partition to run Snakemake head-job

--account <account>

Cluster account to run jobs

--max-run-hours <max_run_hours>

The maximum number of hours that the sbatch script for snakemake is allowed to run on the cluster.

Default:

168

--workflow-profile <workflow_profile>

Directory containing snakemake workflow profile specifying rule resources

Default:

/home/docs/checkouts/readthedocs.org/user_builds/balsamic/checkouts/stable/BALSAMIC/constants/workflow_profile

--qos <qos>

QOS for cluster jobs

Default:

low

Options:

low | normal | high | express

--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

--run-interactively

Run Snakemake job submission interactively instead of submitting the submitter to cluster.

-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