Command line arguments¶
BALSAMIC¶
- BALSAMIC 11.2.0: 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:
11.2.0
- Options:
develop | master | 11.2.0
- --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:
11.2.0
- Options:
develop | master | 11.2.0
- -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/v11.2.0/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/v11.2.0/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
- -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/v11.2.0/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/v11.2.0/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’]