Index Symbols | B Symbols --account BALSAMIC-init command line option BALSAMIC-run-analysis command line option --adapter-trim BALSAMIC-config-case command line option BALSAMIC-config-pon 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 --background-variants BALSAMIC-config-case command line option --balsamic-cache BALSAMIC-config-case command line option BALSAMIC-config-pon command line option --benchmark BALSAMIC-run-analysis 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-germline-snv-observations BALSAMIC-config-case command line option --cancer-somatic-snv-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 --cluster-config BALSAMIC-init command line option BALSAMIC-run-analysis command line option --cosmic-key BALSAMIC-init command line option --disable-variant-caller BALSAMIC-report-deliver command line option BALSAMIC-run-analysis command line option --dragen BALSAMIC-run-analysis 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 --log-level BALSAMIC command line option --mail-type BALSAMIC-init command line option BALSAMIC-run-analysis command line option --mail-user BALSAMIC-init command line option BALSAMIC-run-analysis command line option --no-adapter-trim BALSAMIC-config-case command line option BALSAMIC-config-pon command line option --no-quality-trim BALSAMIC-config-case command line option BALSAMIC-config-pon command line option --no-umi BALSAMIC-config-case command line option BALSAMIC-config-pon 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 --print-files BALSAMIC-report-status command line option --profile BALSAMIC-init command line option BALSAMIC-run-analysis command line option --qos BALSAMIC-init command line option BALSAMIC-run-analysis command line option --quality-trim BALSAMIC-config-case command line option BALSAMIC-config-pon command line option --quiet BALSAMIC-init command line option BALSAMIC-run-analysis 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-mode BALSAMIC-init command line option BALSAMIC-run-analysis command line option --sample-config BALSAMIC-report-deliver command line option BALSAMIC-report-status command line option BALSAMIC-run-analysis command line option --show-only-missing BALSAMIC-report-status 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 --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 BALSAMIC-config-case command line option BALSAMIC-config-pon command line option --umi-trim-length BALSAMIC-config-case command line option BALSAMIC-config-pon command line option --version BALSAMIC command line option BALSAMIC-config-pon command line option -b BALSAMIC-config-case command line option -c BALSAMIC-init command line option -g BALSAMIC-config-case command line option BALSAMIC-config-pon command line option BALSAMIC-init command line option -m BALSAMIC-report-status command line option -o BALSAMIC-init command line option -p BALSAMIC-config-case command line option BALSAMIC-config-pon command line option BALSAMIC-init 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-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-report-status 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 --adapter-trim --analysis-dir --analysis-workflow --background-variants --balsamic-cache --cache-version --cadd-annotations --cancer-germline-snv-observations --cancer-somatic-snv-observations --cancer-somatic-sv-observations --case-id --clinical-snv-observations --clinical-sv-observations --fastq-path --gender --genome-interval --genome-version --gens-coverage-pon --gnomad-min-af5 --no-adapter-trim --no-quality-trim --no-umi --normal-sample-name --panel-bed --pon-cnn --quality-trim --swegen-snv --swegen-sv --tumor-sample-name --umi --umi-trim-length -b -g -p -w BALSAMIC-config-pon command line option --adapter-trim --analysis-dir --balsamic-cache --cache-version --case-id --fastq-path --genome-interval --genome-version --no-adapter-trim --no-quality-trim --no-umi --panel-bed --pon-workflow --quality-trim --umi --umi-trim-length --version -g -p -v BALSAMIC-init command line option --account --cache-version --cluster-config --cosmic-key --force-all --genome-version --mail-type --mail-user --out-dir --profile --qos --quiet --run-analysis --run-mode --snakefile --snakemake-opt -c -g -o -p -q -r -S BALSAMIC-report-deliver command line option --disable-variant-caller --rules-to-deliver --sample-config -r -s BALSAMIC-report-status command line option --print-files --sample-config --show-only-missing -m -p -s BALSAMIC-run-analysis command line option --account --benchmark --cluster-config --disable-variant-caller --dragen --force-all --mail-type --mail-user --profile --qos --quiet --run-analysis --run-mode --sample-config --snakefile --snakemake-opt -p -q -r -s -S