CLI reference¶

BALSAMIC¶

BALSAMIC 7.0.0: Bioinformatic Analysis pipeLine for SomAtic MutatIons in Cancer

BALSAMIC [OPTIONS] COMMAND [ARGS]...

Options

--loglevel <loglevel>¶

Set the level of log output.

Default:	DEBUG
Options:	DEBUG\|INFO\|WARNING\|ERROR\|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

--case-id <case_id>¶: Required Sample id that is used for reporting, naming the analysis jobs, and analysis path

--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

Default:	5

--quality-trim, --no-quality-trim¶

Trim low quality reads in fastq

Default:	True

--adapter-trim, --no-adapter-trim¶

Trim adapters from reads in fastq

Default:	True

-p, --panel-bed <panel_bed>¶: Panel bed file for variant calling.

-b, --background-variants <background_variants>¶: Background set of valid variants for UMI

--balsamic-cache <balsamic_cache>¶: Required Path to BALSAMIC cache

--analysis-dir <analysis_dir>¶: Required Root analysis path to store analysis logs and results. The final path will be analysis-dir/sample-id

-t, --tumor <tumor>¶: Required Fastq files for tumor sample.

-n, --normal <normal>¶: Fastq files for normal sample.

--umiworkflow, --no-umiworkflow¶

Enable running UMI workflow

Default:	True

--tumor-sample-name <tumor_sample_name>¶: Tumor sample name

--normal-sample-name <normal_sample_name>¶: Normal sample name

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

Genome version to prepare reference. Path to genomewill be <outdir>/genome_version

Options:	hg19\|hg38

init¶

Initialize various resources after first installation. - Pull container(s) for BALSAMIC according to matching version - Download and build a reference

BALSAMIC init [OPTIONS]

Options

-o, --outdir, --out-dir <outdir>¶: Required Output directory for ref files.This path will be used as base path for files

-v, --container-version <container_version>¶

Container for BALSAMIC version to download

Default:	7.0.0
Options:	develop\|master\|7.0.0

-f, --force¶

Force re-downloading all containers

Default:	False

-c, --cosmic-key <cosmic_key>¶: Required cosmic db authentication key

-s, --snakefile <snakefile>¶

snakefile for reference generation

Default:	/home/docs/checkouts/readthedocs.org/user_builds/balsamic/checkouts/v7.0.0/BALSAMIC/workflows/reference.smk

-d, --dagfile <dagfile>¶

DAG file for overview

Default:	generate_ref_worflow_graph

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

Genome version to prepare reference. Path to genomewill be <outdir>/genome_version

Options:	hg19\|hg38

-r, --run-analysis¶

By default balsamic run_analysis will run in dry run mode.Raise this flag to make the actual analysis

Default:	False

-f, --force-all¶

Force run all analysis. This is same as snakemake –forceall

Default:	False

--snakemake-opt <snakemake_opt>¶: Pass these options directly to snakemake

-q, --quiet¶: Instruct snakemake to be quiet!No output will be printed

plugins¶

Additional and helper utilities for third party applications

BALSAMIC plugins [OPTIONS] COMMAND [ARGS]...

scout¶

Create a scout config.yaml file

BALSAMIC plugins scout [OPTIONS]

Options

--sample-config <sample_config>¶: Required Sample config file. Output of balsamic config sample

--snv-vcf <snv_vcf>¶: variant caller to load as vcf_cancer

--tumor <tumor>¶: sample name for tumor sample

--normal <normal>¶: sample name for normal sample

--sv-vcf <sv_vcf>¶: variant caller to load as vcf_cancer_sv

--customer-id <customer_id>¶: Required customer id for scout config

target-cov-plot¶

cli for coverage plot sub-command. Creates coverage plots in result_directory.

BALSAMIC plugins target-cov-plot [OPTIONS]

vcfutils¶

Commands to process VCF files

BALSAMIC plugins vcfutils [OPTIONS] COMMAND [ARGS]...

createvcf¶

Filter input variants from reference VCF

BALSAMIC plugins vcfutils createvcf [OPTIONS]

Options

-i, --input_file <input_file>¶: Required tab-seperated reference text file

-r, --reference_file <reference_file>¶: Required cosmic database file

-o, --output_file <output_file>¶: Required Output file name

report¶

Various command to create report, check status, and prepare delivery files

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

deliver¶

cli for deliver sub-command. Writes <case_id>.hk in result_directory.

BALSAMIC report deliver [OPTIONS]

Options

-s, --sample-config <sample_config>¶: Required Sample config file. Output of balsamic config sample

--sample-id-map <sample_id_map>¶: Separated internal sample ID with external ID. Use comma formultiple samples. These IDs MUST exist in sample-config.Syntax: internal_id:sample_type:external_id. e.g. ACC1:tumor:KS454,ACC2:normal:KS556

--case-id-map <case_id_map>¶: Separated internal case ID with external ID.Syntax: gene_panel_name:external_id. e.g. gmck-solid:KSK899:apptag

-a, --analysis-type <analysis_type>¶

Type of analysis to run from input config file.By default it will read from config file, but it will override config fileif it is set here.

Options:	qc\|paired\|single

-r, --rules-to-deliver <rules_to_deliver>¶: Specify a rule to deliver. Delivery mode selected via –delivery-mode option

-m, --delivery-mode <delivery_mode>¶

a: append rules-to-deliver to current delivery options. or r: reset current rules to delivery to only the ones specified

Default:	a
Options:	a\|r

--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’, ‘tnsnv’, ‘tnscope’, ‘tnhaplotyper’, ‘dnascope’, ‘manta’, ‘cnvkit’, ‘vardict’, ‘manta_germline’, ‘haplotypecaller’]

status¶

cli for status sub-command.

BALSAMIC report status [OPTIONS]

Options

-s, --sample-config <sample_config>¶: Required Sample config file. Output of balsamic config sample

-m, --show-only-missing¶

Only show missing files.

Default:	False

-p, --print-files¶

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

Default:	False

run¶

Run BALSAMIC on a provided config file

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

analysis¶

Runs BALSAMIC workflow on the provided sample’s config file

BALSAMIC run analysis [OPTIONS]

Options

-a, --analysis-type <analysis_type>¶

Type of analysis to run from input config file.By default it will read from config file, but itwill override config file if it is set here.

Options:	paired\|single\|umi\|qc

-S, --snake-file <snake_file>¶: Input for a custom snakefile. WARNING: This is for internal testing, and should not be used. Providing a snakefile supersedesanalysis_type option.

-s, --sample-config <sample_config>¶: Required Sample json config file.

--run-mode <run_mode>¶

Run mode to use. By default SLURM will be used to run the analysis. But local runner also available for local computing

Default:	cluster
Options:	local\|cluster

-c, --cluster-config <cluster_config>¶

cluster config json file. (eg- SLURM, QSUB)

Default:	/home/docs/checkouts/readthedocs.org/user_builds/balsamic/checkouts/v7.0.0/BALSAMIC/config/cluster.json

--dragen¶: Enable dragen variant caller

-p, --profile <profile>¶

cluster profile to submit jobs

Options:	slurm\|qsub

--benchmark¶: Profile slurm jobs using the value of this option. Make sure you have slurm profiler enabled in your HPC.

-r, --run-analysis¶

By default balsamic run_analysis will run in dry run mode. Raise thise flag to make the actual analysis

Default:	False

--qos <qos>¶

QOS for sbatch jobs. Passed to /home/docs/checkouts/readthedocs.org/user_builds/balsamic/checkouts/v7.0.0/BALSAMIC/utils/scheduler.py

Default:	low
Options:	low\|normal\|high

-f, --force-all¶

Force run all analysis. This is same as snakemake –forceall

Default:	False

--snakemake-opt <snakemake_opt>¶: Pass these options directly to snakemake

--account, --slurm-account, --qsub-account <account>¶: cluster account to run jobs, ie: slurm_account

--mail-user <mail_user>¶: cluster mail user to send out email. e.g.: slurm_mail_user

-q, --quiet¶: Instruct snakemake to be quiet!No output will be printed

--mail-type <mail_type>¶

cluster mail type to send out email. This will be applied to all jobs and override snakemake settings.

Options:	NONE\|BEGIN\|END\|FAIL\|REQUEUE\|ALL\|TIME_LIMIT

--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’, ‘tnsnv’, ‘tnscope’, ‘tnhaplotyper’, ‘dnascope’, ‘manta’, ‘cnvkit’, ‘vardict’, ‘manta_germline’, ‘haplotypecaller’]