Index

Symbols

--account BALSAMIC-init command line option BALSAMIC-run-analysis command line option --analysis-dir BALSAMIC-config-case command line option BALSAMIC-config-pon command line option --analysis-workflow BALSAMIC-config-case command line option --artefact-snv-observations BALSAMIC-config-case command line option --artefact-sv-observations BALSAMIC-config-case command line option --background-variants BALSAMIC-config-case command line option --balsamic-cache BALSAMIC-config-case command line option BALSAMIC-config-pon command line option --cache-profile BALSAMIC-init command line option --cache-version BALSAMIC-config-case command line option BALSAMIC-config-pon command line option BALSAMIC-init command line option --cadd-annotations BALSAMIC-config-case command line option --cancer-genelist BALSAMIC-config-case command line option --cancer-germline-snv-observations BALSAMIC-config-case command line option --cancer-somatic-snv-observations BALSAMIC-config-case command line option --cancer-somatic-snv-panel-observations BALSAMIC-config-case command line option --cancer-somatic-sv-observations BALSAMIC-config-case command line option --case-id BALSAMIC-config-case command line option BALSAMIC-config-pon command line option --clinical-snv-observations BALSAMIC-config-case command line option --clinical-sv-observations BALSAMIC-config-case command line option --cosmic BALSAMIC-config-case command line option --cust-case-id BALSAMIC-config-case command line option --dragen BALSAMIC-run-analysis command line option --exome BALSAMIC-config-case command line option --fastq-path BALSAMIC-config-case command line option BALSAMIC-config-pon command line option --force-all BALSAMIC-init command line option BALSAMIC-run-analysis command line option --gender BALSAMIC-config-case command line option --genome-interval BALSAMIC-config-case command line option BALSAMIC-config-pon command line option --genome-version BALSAMIC-config-case command line option BALSAMIC-config-pon command line option BALSAMIC-init command line option --gens-coverage-pon BALSAMIC-config-case command line option --gnomad-min-af5 BALSAMIC-config-case command line option --headjob-partition BALSAMIC-init command line option BALSAMIC-run-analysis command line option --log-level BALSAMIC command line option --max-run-hours BALSAMIC-init command line option BALSAMIC-run-analysis command line option --normal-sample-name BALSAMIC-config-case command line option --out-dir BALSAMIC-init command line option --panel-bed BALSAMIC-config-case command line option BALSAMIC-config-pon command line option --pon-cnn BALSAMIC-config-case command line option

--pon-workflow BALSAMIC-config-pon command line option --qos BALSAMIC-init command line option BALSAMIC-run-analysis command line option --quiet BALSAMIC-init command line option BALSAMIC-run-analysis command line option --rescue-snvs BALSAMIC-config-case command line option --rules-to-deliver BALSAMIC-report-deliver command line option --run-analysis BALSAMIC-init command line option BALSAMIC-run-analysis command line option --run-interactively BALSAMIC-init command line option BALSAMIC-run-analysis command line option --run-mode BALSAMIC-init command line option BALSAMIC-run-analysis command line option --sample-config BALSAMIC-report-deliver command line option BALSAMIC-run-analysis command line option --sentieon-install-dir BALSAMIC-config-case command line option BALSAMIC-config-pon command line option --sentieon-license BALSAMIC-config-case command line option BALSAMIC-config-pon command line option --snakefile BALSAMIC-init command line option BALSAMIC-run-analysis command line option --snakemake-opt BALSAMIC-init command line option BALSAMIC-run-analysis command line option --soft-filter-normal BALSAMIC-config-case command line option --swegen-snv BALSAMIC-config-case command line option --swegen-sv BALSAMIC-config-case command line option --tumor-sample-name BALSAMIC-config-case command line option --umi-min-reads BALSAMIC-config-case command line option --version BALSAMIC command line option BALSAMIC-config-pon command line option --workflow-partition BALSAMIC-init command line option BALSAMIC-run-analysis command line option --workflow-profile BALSAMIC-run-analysis command line option -b BALSAMIC-config-case command line option -c BALSAMIC-config-case command line option -g BALSAMIC-config-case command line option BALSAMIC-config-pon command line option BALSAMIC-init command line option -o BALSAMIC-init command line option -p BALSAMIC-config-case command line option BALSAMIC-config-pon command line option -q BALSAMIC-init command line option BALSAMIC-run-analysis command line option -r BALSAMIC-init command line option BALSAMIC-report-deliver command line option BALSAMIC-run-analysis command line option -S BALSAMIC-init command line option BALSAMIC-run-analysis command line option -s BALSAMIC-report-deliver command line option BALSAMIC-run-analysis command line option -v BALSAMIC-config-pon command line option -w BALSAMIC-config-case command line option

B

BALSAMIC command line option --log-level --version BALSAMIC-config-case command line option --analysis-dir --analysis-workflow --artefact-snv-observations --artefact-sv-observations --background-variants --balsamic-cache --cache-version --cadd-annotations --cancer-genelist --cancer-germline-snv-observations --cancer-somatic-snv-observations --cancer-somatic-snv-panel-observations --cancer-somatic-sv-observations --case-id --clinical-snv-observations --clinical-sv-observations --cosmic --cust-case-id --exome --fastq-path --gender --genome-interval --genome-version --gens-coverage-pon --gnomad-min-af5 --normal-sample-name --panel-bed --pon-cnn --rescue-snvs --sentieon-install-dir --sentieon-license --soft-filter-normal --swegen-snv --swegen-sv --tumor-sample-name --umi-min-reads -b -c -g -p -w BALSAMIC-config-pon command line option --analysis-dir --balsamic-cache --cache-version --case-id --fastq-path --genome-interval --genome-version --panel-bed --pon-workflow --sentieon-install-dir --sentieon-license --version -g -p -v

BALSAMIC-init command line option --account --cache-profile --cache-version --force-all --genome-version --headjob-partition --max-run-hours --out-dir --qos --quiet --run-analysis --run-interactively --run-mode --snakefile --snakemake-opt --workflow-partition -g -o -q -r -S BALSAMIC-report-deliver command line option --rules-to-deliver --sample-config -r -s BALSAMIC-run-analysis command line option --account --dragen --force-all --headjob-partition --max-run-hours --qos --quiet --run-analysis --run-interactively --run-mode --sample-config --snakefile --snakemake-opt --workflow-partition --workflow-profile -q -r -s -S