Index

Symbols

--account BALSAMIC-run-analysis command line option --adapter-trim BALSAMIC-config-case command line option --analysis-dir <analysis_dir> BALSAMIC-config-case command line option --analysis-type <analysis_type> BALSAMIC-report-deliver command line option BALSAMIC-run-analysis command line option --background-variants <background_variants> BALSAMIC-config-case command line option --balsamic-cache <balsamic_cache> BALSAMIC-config-case command line option --benchmark BALSAMIC-run-analysis command line option --case-id <case_id> BALSAMIC-config-case command line option --case-id-map <case_id_map> BALSAMIC-report-deliver command line option --cluster-config <cluster_config> BALSAMIC-run-analysis command line option --container-version <container_version> BALSAMIC-init command line option --cosmic-key <cosmic_key> BALSAMIC-init command line option --customer-id <customer_id> BALSAMIC-plugins-scout command line option --dagfile <dagfile> BALSAMIC-init command line option --delivery-mode <delivery_mode> BALSAMIC-report-deliver command line option --disable-variant-caller <disable_variant_caller> BALSAMIC-report-deliver command line option BALSAMIC-run-analysis command line option --dragen BALSAMIC-run-analysis command line option --force BALSAMIC-init command line option --force-all BALSAMIC-init command line option BALSAMIC-run-analysis command line option --genome-version <genome_version> BALSAMIC-config-case command line option BALSAMIC-init command line option --input_file <input_file> BALSAMIC-plugins-vcfutils-createvcf command line option --loglevel <loglevel> BALSAMIC command line option --mail-type <mail_type> BALSAMIC-run-analysis command line option --mail-user <mail_user> BALSAMIC-run-analysis command line option --no-adapter-trim BALSAMIC-config-case command line option --no-quality-trim BALSAMIC-config-case command line option --no-umi BALSAMIC-config-case command line option --no-umiworkflow BALSAMIC-config-case command line option --normal <normal> BALSAMIC-config-case command line option BALSAMIC-plugins-scout command line option --normal-sample-name <normal_sample_name> BALSAMIC-config-case command line option --out-dir <outdir> BALSAMIC-init command line option --outdir BALSAMIC-init command line option --output_file <output_file> BALSAMIC-plugins-vcfutils-createvcf command line option --panel-bed <panel_bed> BALSAMIC-config-case command line option --print-files BALSAMIC-report-status command line option --profile <profile> BALSAMIC-run-analysis command line option --qos <qos> BALSAMIC-run-analysis command line option --qsub-account <account> BALSAMIC-run-analysis command line option --quality-trim BALSAMIC-config-case command line option --quiet BALSAMIC-init command line option BALSAMIC-run-analysis command line option --reference_file <reference_file> BALSAMIC-plugins-vcfutils-createvcf command line option --rules-to-deliver <rules_to_deliver> BALSAMIC-report-deliver command line option

--run-analysis BALSAMIC-init command line option BALSAMIC-run-analysis command line option --run-mode <run_mode> BALSAMIC-run-analysis command line option --sample-config <sample_config> BALSAMIC-plugins-scout command line option BALSAMIC-report-deliver command line option BALSAMIC-report-status command line option BALSAMIC-run-analysis command line option --sample-id-map <sample_id_map> BALSAMIC-report-deliver command line option --show-only-missing BALSAMIC-report-status command line option --slurm-account BALSAMIC-run-analysis command line option --snake-file <snake_file> BALSAMIC-run-analysis command line option --snakefile <snakefile> BALSAMIC-init command line option --snakemake-opt <snakemake_opt> BALSAMIC-init command line option BALSAMIC-run-analysis command line option --snv-vcf <snv_vcf> BALSAMIC-plugins-scout command line option --sv-vcf <sv_vcf> BALSAMIC-plugins-scout command line option --tumor <tumor> BALSAMIC-config-case command line option BALSAMIC-plugins-scout command line option --tumor-sample-name <tumor_sample_name> BALSAMIC-config-case command line option --umi BALSAMIC-config-case command line option --umi-trim-length <umi_trim_length> BALSAMIC-config-case command line option --umiworkflow BALSAMIC-config-case command line option --version BALSAMIC command line option -a BALSAMIC-report-deliver command line option BALSAMIC-run-analysis command line option -b BALSAMIC-config-case command line option -c BALSAMIC-init command line option BALSAMIC-run-analysis command line option -d BALSAMIC-init command line option -f BALSAMIC-init command line option, [1] BALSAMIC-run-analysis command line option -g BALSAMIC-config-case command line option BALSAMIC-init command line option -i BALSAMIC-plugins-vcfutils-createvcf command line option -m BALSAMIC-report-deliver command line option BALSAMIC-report-status command line option -n BALSAMIC-config-case command line option -o BALSAMIC-init command line option BALSAMIC-plugins-vcfutils-createvcf command line option -p BALSAMIC-config-case command line option BALSAMIC-report-status command line option BALSAMIC-run-analysis command line option -q BALSAMIC-init command line option BALSAMIC-run-analysis command line option -r BALSAMIC-init command line option BALSAMIC-plugins-vcfutils-createvcf command line option BALSAMIC-report-deliver command line option BALSAMIC-run-analysis command line option -S BALSAMIC-run-analysis command line option -s BALSAMIC-init command line option BALSAMIC-report-deliver command line option BALSAMIC-report-status command line option BALSAMIC-run-analysis command line option -t BALSAMIC-config-case command line option -v BALSAMIC-init command line option

B

BALSAMIC command line option --loglevel <loglevel> --version BALSAMIC-config-case command line option --adapter-trim --analysis-dir <analysis_dir> --background-variants <background_variants> --balsamic-cache <balsamic_cache> --case-id <case_id> --genome-version <genome_version> --no-adapter-trim --no-quality-trim --no-umi --no-umiworkflow --normal <normal> --normal-sample-name <normal_sample_name> --panel-bed <panel_bed> --quality-trim --tumor <tumor> --tumor-sample-name <tumor_sample_name> --umi --umi-trim-length <umi_trim_length> --umiworkflow -b -g -n -p -t BALSAMIC-init command line option --container-version <container_version> --cosmic-key <cosmic_key> --dagfile <dagfile> --force --force-all --genome-version <genome_version> --out-dir <outdir> --outdir --quiet --run-analysis --snakefile <snakefile> --snakemake-opt <snakemake_opt> -c -d -f, [1] -g -o -q -r -s -v BALSAMIC-plugins-scout command line option --customer-id <customer_id> --normal <normal> --sample-config <sample_config> --snv-vcf <snv_vcf> --sv-vcf <sv_vcf> --tumor <tumor>

BALSAMIC-plugins-vcfutils-createvcf command line option --input_file <input_file> --output_file <output_file> --reference_file <reference_file> -i -o -r BALSAMIC-report-deliver command line option --analysis-type <analysis_type> --case-id-map <case_id_map> --delivery-mode <delivery_mode> --disable-variant-caller <disable_variant_caller> --rules-to-deliver <rules_to_deliver> --sample-config <sample_config> --sample-id-map <sample_id_map> -a -m -r -s BALSAMIC-report-status command line option --print-files --sample-config <sample_config> --show-only-missing -m -p -s BALSAMIC-run-analysis command line option --account --analysis-type <analysis_type> --benchmark --cluster-config <cluster_config> --disable-variant-caller <disable_variant_caller> --dragen --force-all --mail-type <mail_type> --mail-user <mail_user> --profile <profile> --qos <qos> --qsub-account <account> --quiet --run-analysis --run-mode <run_mode> --sample-config <sample_config> --slurm-account --snake-file <snake_file> --snakemake-opt <snakemake_opt> -a -c -f -p -q -r -S -s