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CLI reference

The ferro command groups its work into subcommands. Run ferro <command> --help for the full, authoritative options of any one — this page is a map, not a substitute.

Core

CommandWhat it does
parseParse and validate an HGVS description (no reference needed).
normalizeRewrite descriptions into canonical form (needs a reference). See Normalize variants.
projectRe-express a variant on a chosen output axis (g / c / n / p / r).
explainExplain an error or warning code (e.g. ferro explain W3003).

Reference data

CommandWhat it does
prepareDownload and assemble reference data. See Reference data.
checkVerify a reference directory is ready (optionally pre-build the cache).
convert-gffConvert a GFF3/GTF annotation to transcripts.json.
build-transcriptBuild a single-exon transcripts.json from a FASTA + CDS coordinates.

VCF and interchange

CommandWhat it does
annotate-vcfAnnotate a VCF file with HGVS notation.
vcf-to-hgvs / hgvs-to-vcfConvert between VCF and HGVS.
extract-hgvsExtract HGVS patterns from VEP-annotated VCF files.
liftoverLift genomic coordinates between genome builds.

Generation and prediction

CommandWhat it does
generateGenerate an HGVS description from components.
describeGenerate a description from reference and observed sequences.
effectPredict the protein effect of a variant.
backtranslateBacktranslate a protein variant to possible DNA variants.

Common options

Most commands accept -i/--input <file> (one description per line) and -o/--output <file>. The output format is set with -f/--format, and the accepted values depend on the command: text|json for parse and project, text|json|tsv for normalize, and text|json|markdown for explain. Commands that normalize also accept --reference <dir> and --error-mode <strict|lenient|silent>.