Options Reference

Subcommands

Subcommand	Description
run-pipeline	Normalize and filter a VCF file (default if omitted)
generate-inclusion-bed	Merge BED files into a combined inclusion region
generate-exclusion-bed	Merge BED files into a combined exclusion region

Running hardnormly.sh [options] without a subcommand is equivalent to hardnormly.sh run-pipeline [options].

---

run-pipeline

Input / Output

Flag	Type	Default	Description
-v, --vcf	FILE	required	Input VCF file (.vcf or .vcf.gz)
-f, --fasta	FILE	required	Reference FASTA file for normalization
-o, --output	FILE	stdout	Output VCF file. Extension determines format: .vcf.gz writes compressed, .vcf writes plain text

Region Filtering

Flag	Type	Default	Description
-b, --include-bed	FILE	—	BED file for inclusion regions. Repeatable: multiple files are intersected
-e, --exclude-bed	FILE	—	BED file for exclusion regions. Repeatable: multiple files are unioned
-g, --genome	FILE	—	Genome file for bedtools slop. Skips UCSC MySQL fetch if provided
--genome-build	STRING	hg19	Genome build for UCSC fetch (e.g., hg19, hg38)
--slop	INT	20	Region padding in base pairs applied to inclusion BED regions

Variant Filtering

Flag	Type	Default	Description
--caller	STRING	—	Auto-select filter file: gatk or freebayes
--filters-file	FILE	—	Custom filter file (overrides --caller if both provided)
--filters	STRING	—	Inline filter: "name action expression". Repeatable
--strip-annotations	STRING	—	Comma-separated INFO fields to remove before filtering (e.g., INFO/CSQ,INFO/ANN)
--only-pass	FLAG	off	Remove filtered variants, keep only PASS in output

Stats and Plots

Flag	Type	Default	Description
--generate-stats	FLAG	off	Generate bcftools stats file alongside output
--plot-stats	FLAG	off	Plot stats (requires --generate-stats and --plot-output-dir)
--plot-output-dir	DIR	—	Directory for plot output files

Runtime

Flag	Type	Default	Description
--auto-index	FLAG	off	Auto-index output if compressed (.vcf.gz → .vcf.gz.tbi)
--tmp-dir	DIR	auto	Custom temporary directory (default: system mktemp)
--no-cleanup	FLAG	off	Preserve temporary directory after run
--log-file	FILE	—	Write log messages to file instead of stdout
--debug	FLAG	off	Enable verbose debug output (set -x tracing)

Info

Flag	Description
--version	Print version and exit
-h, --help	Print usage help and exit

---

generate-inclusion-bed

Merge one or more BED files into a combined inclusion region file with slop padding.

Flag	Type	Default	Description
-b, --include-bed	FILE	required	Input BED file. Repeatable
-g, --genome	FILE	required	Genome file for slop operation
-o, --output	FILE	required	Output merged BED file
--slop	INT	20	Region padding in base pairs
-v, --verbose	FLAG	off	Show progress messages
-h, --help	FLAG	—	Show subcommand help

---

generate-exclusion-bed

Merge one or more BED files into a combined exclusion region file.

Flag	Type	Default	Description
-e, --exclude-bed	FILE	required	Input BED file. Repeatable
-o, --output	FILE	required	Output merged BED file
-v, --verbose	FLAG	off	Show progress messages
-h, --help	FLAG	—	Show subcommand help