Standalone Version

Contents

Downloads

FABIAN-variant is primarily a web application. The standalone version supports high-throughput analysis, integration into local pipelines, and the processing of sensitive data that cannot be sent to an external server. It is distributed as a self-contained executable with no additional dependencies.

Note: Downloads for the updated standalone version will be available again by 10 July 2026.

• Linux
  • fabian_standalone
  • download_genomes.sh
  • LICENSE (MIT), THIRD-PARTY-LICENSES
   
• macOS
  • fabian_standalone_macos (Universal)
  • download_genomes.sh
  • LICENSE (MIT), THIRD-PARTY-LICENSES
  • First run: 'Right-click > Open', or
    xattr -d com.apple.quarantine fabian_standalone_macos
   
• Windows
  • fabian_standalone.exe
  • download_genomes.bat
  • LICENSE (MIT), THIRD-PARTY-LICENSES
   

Last updated: 7 July 2026.

The application is written in C++11 and has no special hardware requirements. Processing time scales linearly with the number of variants and selected models. TFFMs take longer to evaluate than PWMs.

Command-line interface

The standalone tool supports two modes:

• Search with two sequences

  [--mouse] <ref-sequence> <alt-sequence> "<filters-and-TFs>" [output-file]

  Argument	Description
  [--mouse]	Use mouse TF models instead of human
  <ref-sequence>	Reference sequence
  <alt-sequence>	Variant sequence
  "<filters-and-TFs>"	Quoted string of filters and TF selection (see next section)
  [output-file]	Optional output path (default: stdout)

   
• Search with VCF or sequence list file

  [--mouse] --file <file> [--genome <path>] "<filters-and-TFs>" [output-file]

  Argument	Description
  [--mouse]	Use mouse TF models instead of human
  --file <file>	Input file in VCF or sequence list format
  --genome <path>	Path to genome FASTA files (required for VCF)
  "<filters-and-TFs>"	Quoted string of filters and TF selection (see next section)
  [output-file]	Optional output path (default: stdout)

Filters and TF selection

The <filters-and-TFs> argument is a quoted string containing source filters, model filters, and the TF selection. Filters must come before TF names. The standalone binary embeds prediction models from openly licensed sources.

Option	Description
Optional source filters (combine any number)
--JASPAR-TFFM	JASPAR 2024 TFFMs
--JASPAR-PWM	JASPAR 2026 PWM models
--HOCOMOCO	HOCOMOCO v14 models
--SwissRegulon	SwissRegulon models
--SELEX	SELEX collection models (subset)
Optional filters
--human-models	Only use models derived from human data
--mouse-models	Only use models derived from mouse data
--no-heterodimers	Exclude heterodimer TFs (e.g. JUND::FOS)
TF selection (one required, must come last)
--all	Analyse all transcription factors
TF1 TF2 ...	Analyse specific TFs (space-separated, must be last)

Example commands

• Analyse a single sequence pair:

  ./fabian_standalone ATCGATCGATCGATCG ATCGATCGATCGATGG "--JASPAR-PWM --all"

   
• Analyse specific transcription factors:

  ./fabian_standalone ATCGATCGATCGATCG ATCGATCGATCGATGG "--JASPAR-PWM SP1 TP53 MYC"

   
• Analyse a VCF file (requires genome):

  ./fabian_standalone --file input.vcf --genome data/hg38 "--JASPAR-PWM --all" fabian.data

   
• Process a sequence list file (no genome required):

  ./fabian_standalone --file input.seqlist "--JASPAR-TFFM --HOCOMOCO --all"

   

Genome data

Genome data is only required when processing VCF files with --file. The download scripts fetch FASTA files for all supported assemblies and save them to data/hg38, data/hg19, etc. Alternatively, chromosome files can be downloaded manually from:

• https://hgdownload.cse.ucsc.edu/goldenPath/hg38/chromosomes/
• https://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/
• https://hgdownload.cse.ucsc.edu/goldenPath/mm39/chromosomes/
• https://hgdownload.cse.ucsc.edu/goldenPath/mm10/chromosomes/

Only the assembly to which the VCF file was aligned is required.

Input formats

• VCF format
  • Standard VCF format. Minimal required columns are CHROM, POS, REF, and ALT:

    • #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
      2	127418425	.	T	C	.	.	.
      10	6051177	.	G	A	.	.	.

     
• Sequence list format
  • Tab-separated file with reference and variant sequences, one pair per line (extension .seqlist):

    • AGTCCTTGGCTCTTATCTTGGAAGCACAGGC	AGTCCTTGGCTCTTACCTTGGAAGCACAGGC
      TCGAGGCCCTGAGCTCCCGGGGAGTTTTTAC	TCGAGGCCCTGAGCTTCCGGGGAGTTTTTAC

     

Output format

Output is a tab-separated file with per-model predictions, identical to the downloadable results from the web version:

variant tf model_id database ref_score alt_score start_ref end_ref start_alt end_alt strand_ref strand_alt prediction score

See the documentation for column descriptions.

Contact

For questions about the standalone version, please email robin.steinhaus (at) bih-charite.de or submit a ticket via email using this link.