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CLI Reference

The full command tree, generated from the live vflank Typer app.

vflank

Variant-aware flanking-sequence extraction and masking for ddPCR assay design.

Usage:

console $ vflank [OPTIONS] COMMAND [ARGS]...

Options:

  • --version: Print the vflank version and exit.
  • -v, --verbose: Enable DEBUG logging.
  • -q, --quiet: Only show warnings and errors.
  • --debug: DEBUG logging + rich tracebacks.
  • --help: Show this message and exit.

Commands:

  • version: Print the vflank version.
  • small: Small-variant (SNP/indel) flank extraction.
  • fusion: Structural-variant junction extraction.

vflank version

Print the vflank version.

Usage:

console $ vflank version [OPTIONS]

Options:

  • --help: Show this message and exit.

vflank small

Small-variant (SNP/indel) flank extraction.

Usage:

console $ vflank small [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • run: Extract flanking sequences for every...
  • inspect: Print column names and a data preview...
  • list-vcf: Show which per-chromosome VCFs were found...

vflank small run

Extract flanking sequences for every variant in a MAF and write a FASTA.

Each variant yields a raw record and a Masked record. Common population SNPs (gnomAD, AF >= --af-threshold) are masked; with --bam/--bam-map the Masked record is the per-sample patient consensus instead (one record per (variant, sample); sample is added to the header). Chromosome notation is auto-detected from the FASTA and VCFs.

Usage:

console $ vflank small run [OPTIONS] MAF_FILE

Arguments:

  • MAF_FILE: Input variants: a MAF (TCGA/MSK TSV) or a VCF/BCF (.vcf/.vcf.gz/.bcf, auto-detected, read sites-only). [required]

Options:

  • -r, --ref-genome PATH: Indexed reference FASTA (.fai required). Required unless --ref-source api.
  • --ref-source TEXT: Reference backend: file (local FASTA, default) or api (UCSC, no download). [default: file]
  • -d, --pop-vcf-dir PATH: Directory of per-chromosome gnomAD VCF bgz files. Omit to skip masking.
  • -g, --genome-build TEXT: hg19 (GRCh37, gnomAD v2.1.1) or hg38 (GRCh38, gnomAD v4). [default: hg19]
  • -f, --flank INTEGER RANGE: Bases on each side of the variant. [default: 200; 1<=x<=10000]
  • --af-threshold FLOAT RANGE: Min population AF to mask a SNP. [default: 0.001; 0.0<=x<=1.0]
  • --pop-data TEXT: gnomAD data to mask against: genome (default), exome, or both (union). [default: genome]
  • --pop-source TEXT: Masking backend: vcf (local gnomAD VCFs) or api (gnomAD GraphQL, no download). [default: vcf]
  • -o, --output PATH: Output FASTA file. [default: flanking_sequences.fasta]
  • --report PATH: Write a per-variant TSV run report (stats + table) to this path.
  • --emit-primer3 PATH: Also write a Primer3 Boulder-IO input file (one record per variant).
  • -s, --samples TEXT: Comma-separated Tumor_Sample_Barcode IDs to include.
  • --samples-file PATH: File of sample IDs, one per line (# comments allowed).
  • --chrom-col TEXT: [default: Chromosome]
  • --start-col TEXT: [default: Start_Position]
  • --end-col TEXT: [default: End_Position]
  • --ref-col TEXT: [default: Reference_Allele]
  • --alt-col TEXT: [default: Tumor_Seq_Allele2]
  • --gene-col TEXT: [default: Hugo_Symbol]
  • --prot-col TEXT: [default: HGVSp_Short]
  • --cdna-col TEXT: [default: HGVSc]
  • --sample-col TEXT: [default: Tumor_Sample_Barcode]
  • --uppercase / --no-uppercase: Uppercase flanking sequences. [default: uppercase]
  • --dedup / --no-dedup: Emit one record per unique variant (CHR_POS_REF_ALT), collapsing samples. [default: dedup]
  • --bam PATH: Single-sample BAM for patient consensus (modes C/D).
  • --bam-map PATH: TSV (Tumor_Sample_Barcodebam_path) for cohort consensus.
  • --bam-min-depth INTEGER: Min depth to trust a base. [default: 20]
  • --bam-call-fract FLOAT: Fraction to call a base. [default: 0.9]
  • --bam-het-char TEXT: Het output: N or iupac. [default: N]
  • --bam-lowcov TEXT: Low-coverage base: n (mask) | reference | gnomad (default: REF + gnomAD). [default: gnomad]
  • --bam-min-baseq INTEGER: [default: 20]
  • --bam-min-mapq INTEGER: [default: 20]
  • --require-coverage FLOAT RANGE: Flag BAM-consensus variants whose flanks are < this fraction covered (0=off). [default: 0.0; 0.0<=x<=1.0]
  • --help: Show this message and exit.

vflank small inspect

Print column names and a data preview without running any analysis.

Usage:

console $ vflank small inspect [OPTIONS] MAF_FILE

Arguments:

  • MAF_FILE: MAF or VCF file to preview [required]

Options:

  • -n, --rows INTEGER RANGE: Data rows to show. [default: 3; 1<=x<=20]
  • --help: Show this message and exit.

vflank small list-vcf

Show which per-chromosome VCFs were found (and which are missing) per data kind.

Usage:

console $ vflank small list-vcf [OPTIONS] POP_VCF_DIR

Arguments:

  • POP_VCF_DIR: Directory of gnomAD per-chromosome VCF bgz files. [required]

Options:

  • -g, --genome-build TEXT: hg19 or hg38 [default: hg19]
  • --pop-data TEXT: Coverage to check: genome, exome, or both. [default: genome]
  • --help: Show this message and exit.

vflank fusion

Structural-variant junction extraction.

Usage:

console $ vflank fusion [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • run: Build fusion-junction sequences for a...

vflank fusion run

Build fusion-junction sequences for a breakpoint table and write a FASTA.

Usage:

console $ vflank fusion run [OPTIONS] SV_FILE

Arguments:

  • SV_FILE: Breakpoint TSV (chr1 pos1 str1 chr2 pos2 str2). [required]

Options:

  • -r, --ref-genome PATH: Indexed reference FASTA (.fai required). Required unless --ref-source api.
  • --ref-source TEXT: Reference backend: file (local FASTA, default) or api (UCSC, no download). [default: file]
  • -g, --genome-build TEXT: hg19 or hg38. [default: hg19]
  • -f, --flank INTEGER RANGE: Bases taken from each partner (junction is up to 2x this). [default: 200; 1<=x<=10000]
  • -d, --pop-vcf-dir PATH: Directory of gnomAD VCFs to mask junction flanks. Omit to skip masking.
  • --pop-data TEXT: gnomAD data to mask against: genome, exome, or both. [default: genome]
  • --pop-source TEXT: Masking backend: vcf or api (no download). [default: vcf]
  • --af-threshold FLOAT RANGE: Min population AF to mask a SNP. [default: 0.001; 0.0<=x<=1.0]
  • -o, --output PATH: Output FASTA file. [default: fusion_junctions.fasta]
  • --emit-primer3 PATH: Also write a Primer3 Boulder-IO input file (one record per junction).
  • --bam PATH: Single-sample BAM for patient consensus of the junction flanks.
  • --bam-map PATH: TSV (samplebam_path) for per-fusion consensus.
  • --bam-min-depth INTEGER: [default: 20]
  • --bam-call-fract FLOAT: [default: 0.9]
  • --bam-het-char TEXT: Het output: N or iupac. [default: N]
  • --bam-lowcov TEXT: Low-coverage base: n | reference | gnomad. [default: gnomad]
  • --bam-min-baseq INTEGER: [default: 20]
  • --bam-min-mapq INTEGER: [default: 20]
  • --chr1-col TEXT: [default: chr1]
  • --pos1-col TEXT: [default: pos1]
  • --str1-col TEXT: [default: str1]
  • --chr2-col TEXT: [default: chr2]
  • --pos2-col TEXT: [default: pos2]
  • --str2-col TEXT: [default: str2]
  • --name-col TEXT: [default: name]
  • --sample-col TEXT: [default: sample]
  • --help: Show this message and exit.