Command line arguments

BALSAMIC

BALSAMIC 12.0.2: Bioinformatic Analysis pipeLine for

SomAtic MutatIons in Cancer

BALSAMIC [OPTIONS] COMMAND [ARGS]...

Options

--loglevel <loglevel>

Set the level of log output.

Default:

INFO

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

--gender <gender>

Case associated gender

Default:

female

Options:

female | male

--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

--pon-cnn <pon_cnn>

Panel of normal reference (.cnn) for cnvkit

--balsamic-cache <balsamic_cache>

Required Path to BALSAMIC cache

--container-version <container_version>

Container for BALSAMIC version to download

Default:

12.0.2

Options:

develop | master | 12.0.2

--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.

--tumor-sample-name <tumor_sample_name>

Tumor sample name

--normal-sample-name <normal_sample_name>

Normal sample name

--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)

--cancer-all-snv-observations <cancer_all_snv_observations>

VCF path of cancer 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)

--swegen-snv <swegen_snv>

VCF path of Swegen SNV frequency database (WGS analysis workflow)

--swegen-sv <swegen_sv>

VCF path of Swegen SV frequency database (WGS analysis workflow)

-g, --genome-version <genome_version>

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

Options:

hg19 | hg38 | canfam3

-w, --analysis-workflow <analysis_workflow>

Analysis workflow to run. By default: “balsamic” only workflow will be running. If you want to run both balsamic and UMI workflow together for panel data; choose “balsamic-umi” option

Default:

balsamic

Options:

balsamic | balsamic-umi | balsamic-qc

pon

Create a sample config file for PON analysis

BALSAMIC config pon [OPTIONS]

Options

--case-id <case_id>

Required Sample id used for reporting analysis

--umi, --no-umi

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

Default:

True

--umi-trim-length <umi_trim_length>

Trimming first N bases from reads in fastq file

Default:

5

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

Trimming low quality reads in fastq file

Default:

True

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

Preprocess fastq reads by trimming adapters

Default:

True

-p, --panel-bed <panel_bed>

Panel bed file for calculating target regions.

--balsamic-cache <balsamic_cache>

Required Path to BALSAMIC cache

--analysis-dir <analysis_dir>

Required Root analysis path directory.

--fastq-path <fastq_path>

Required Path directing to list of PON fastq samples.

-g, --genome-version <genome_version>

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

Options:

hg19

-v, --version <version>

Version of the PON file to be generated

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:

12.0.2

Options:

develop | master | 12.0.2

-f, --force

Force re-downloading all containers

Default:

False

-c, --cosmic-key <cosmic_key>

cosmic db authentication key

-s, --snakefile <snakefile>

snakefile for reference generation

-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 | canfam3

-r, --run-analysis

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

Default:

False

--run-mode <run_mode>

Run mode to use. By default SLURM will be used to generate the balsamic_cacheAlternatively, option for local computing

Default:

cluster

Options:

local | cluster

--cluster-config <cluster_config>

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

Default:

/home/docs/checkouts/readthedocs.org/user_builds/balsamic/checkouts/v12.0.2/BALSAMIC/config/reference_cluster.json

-p, --profile <profile>

cluster profile to submit jobs

Options:

slurm | qsub

--account, --slurm-account, --qsub-account <account>

cluster account to run jobs, ie: slurm_account

--qos <qos>

QOS for sbatch jobs. Passed to /home/docs/checkouts/readthedocs.org/user_builds/balsamic/checkouts/v12.0.2/BALSAMIC/utils/scheduler.py

Default:

low

Options:

low | normal | high | express

--mail-user <mail_user>

cluster mail user to send out email. e.g.: slurm_mail_user

--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

-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

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

Specify a rule to deliver. Delivery mode selected via –delivery-mode option.Current available rules to deliver are: multiqc, collect_custom_qc_metrics, cnv_report, mergeBam_tumor, mergeBam_normal, mergeBam_tumor_umiconsensus, mergeBam_normal_umiconsensus, vep_germline_tumor, vep_germline_normal, vcfheader_rename_germline, 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, vcf2cytosure_convert_tumor_only, vcf2cytosure_convert_tumor_normal, cnvkit_single, cnvkit_paired, vcf2cytosure_convert, tmb_calculation

-m, --delivery-mode <delivery_mode>

a: append rules-to-deliver to current delivery options. 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’, ‘tnscope’, ‘dnascope’, ‘manta’, ‘cnvkit’, ‘vardict’, ‘manta_germline’, ‘haplotypecaller’, ‘dellysv’, ‘tiddit’, ‘dellycnv’, ‘ascat’, ‘cnvpytor’, ‘svdb’]

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

-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/v12.0.2/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/v12.0.2/BALSAMIC/utils/scheduler.py

Default:

low

Options:

low | normal | high | express

-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’, ‘tnscope’, ‘dnascope’, ‘manta’, ‘cnvkit’, ‘vardict’, ‘manta_germline’, ‘haplotypecaller’, ‘dellysv’, ‘tiddit’, ‘dellycnv’, ‘ascat’, ‘cnvpytor’, ‘svdb’]