Command line arguments

BALSAMIC

Balsamic 15.0.0: 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

Create a sample config file from input sample data

BALSAMIC config case [OPTIONS]

Options

--adapter-trim, --no-adapter-trim

Trim adapters from reads in FASTQ file

Default:

True

--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

-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:

15.0.0

--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

--quality-trim, --no-quality-trim

Trim low quality reads in FASTQ file

Default:

True

--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, --no-umi

UMI processing steps for samples with UMI tags. For WGS cases, UMI is always disabled.

Default:

True

--umi-trim-length <umi_trim_length>

Trim N bases from reads in FASTQ file

Default:

5

pon

Create a sample config file for PON analysis

BALSAMIC config pon [OPTIONS]

Options

--adapter-trim, --no-adapter-trim

Trim adapters from reads in FASTQ file

Default:

True

--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:

15.0.0

--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.

-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

--quality-trim, --no-quality-trim

Trim low quality reads in FASTQ file

Default:

True

--umi, --no-umi

UMI processing steps for samples with UMI tags. For WGS cases, UMI is always disabled.

Default:

True

--umi-trim-length <umi_trim_length>

Trim N bases from reads in FASTQ file

Default:

5

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:

15.0.0

--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 | qsub

--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’, ‘manta_germline’, ‘haplotypecaller’, ‘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 | mergeBam_tumor_umiconsensus | mergeBam_normal_umiconsensus | bam_compress_tumor | bam_compress_normal | vcfheader_rename_germline | vep_annotate_germlineVAR_tumor | vep_annotate_germlineVAR_normal | bcftools_view_split_variant | bcftools_filter_tnscope_research_tumor_only | bcftools_filter_tnscope_research_tumor_normal | bcftools_filter_tnscope_clinical_tumor_only | bcftools_filter_tnscope_clinical_tumor_normal | vardict_merge | bcftools_filter_vardict_research_tumor_only | bcftools_filter_vardict_research_tumor_normal | bcftools_filter_vardict_clinical_tumor_only | bcftools_filter_vardict_clinical_tumor_normal | sentieon_tnscope_umi | sentieon_tnscope_umi_tn | bcftools_filter_TNscope_umi_research_tumor_only | bcftools_filter_TNscope_umi_research_tumor_normal | bcftools_filter_TNscope_umi_clinical_tumor_only | bcftools_filter_TNscope_umi_clinical_tumor_normal | 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 | 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 | qsub

--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’, ‘manta_germline’, ‘haplotypecaller’, ‘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