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