Gauchian-enrich

  

A variant annotation toolkit for the GBA gene variants detected from the Illumina/Gauchian tool.

Key Features

• Transforms basic variant calls: Converts raw output from Illumina Gauchian into richly annotated, interpretation-ready variants. It provides detailed biological context for genetic variants, including transcript information, precise genomic coordinates (gDNA/cDNA/protein), and a clear assessment of their functional impact.
• Detailed Functional Analysis: Goes beyond basic variant calls to classify mutations (e.g., missense) and suggests potential alternative causes, such as multiple nucleotide variants (MNVs), that might lead to the same protein change.
• Rich Output Format: The tool generates a highly detailed, tabular output designed for seamless integration into existing bioinformatics pipelines. The output includes essential fields like CHROM, POS, REF, and ALT, making it easily parseable and ideal for downstream analysis.

Setup (recommended)

To use the gauchian_enrich utility, ensure Docker is installed on your system. Then, pull the Docker image:

docker pull ghcr.io/maurya-anand/gauchian-enrich

Manual setup

If you prefer to install and configure the gauchian_enrich utility locally without using Docker, you can use the provided Makefile. This will ensure all dependencies are installed and the required configuration files are set up.

Steps for Manual Installation

1. Ensure the following tools are installed on your system:

   • samtools
   • wget
   • gunzip
   • pip or pip3
   • Perl module Parallel::ForkManager

2. Run the following command to install and configure the utility:

make install

Usage

Step 1 : Run the Illumina/Gauchian tool to obtain the .tsv and .json output.

Step 2 : Use the .tsv ouput file from the previous step as an input to gauchian_enrich utility.

Command-Line Options

• --input or -i: Specify the input .tsv file generated by the Gauchian tool.
• --output or -o: Specify the output file path. If omitted, a default output file will be created based on the input file name.
• --help or -h: Display usage instructions.
• --version or -v: Display the version of the gauchian_enrich tool.

Note

The gauchian_enrich utility performs reverse annotation using the transvar tool and the hg38 reference genome. The reverse annotation process relies on the hg38 reference genome file (/ref/hg38.fa). The Docker image for gauchian_enrich comes preconfigured with transvar and the hg38 reference genome, eliminating the need for users to download or configure the reference genome manually.

Example usage

To display usage instructions:

docker run ghcr.io/maurya-anand/gauchian-enrich gauchian_enrich --help

To execute the tool using the given example data:

docker run -u $(id -u):$(id -g) -it \
    -v ${PWD}/example:/example \
    ghcr.io/maurya-anand/gauchian-enrich \
    gauchian_enrich -i /example/test.gauchian.tsv -o /example/test.gauchian.annotated.tsv

Example data

Input

Sample	is_biallelic(GBAP1-like_variant_exon9-11)	is_carrier(GBAP1-like_variant_exon9-11)	CN(GBA+GBAP1)	deletion_breakpoint_in_GBA	GBAP1-like_variant_exon9-11	other_unphased_variants
NA20815.final	FALSE	TRUE	4	N/A	L483P/

Output

Sample	is_biallelic(GBAP1-like_variant_exon9-11)	is_carrier(GBAP1-like_variant_exon9-11)	CN(GBA+GBAP1)	deletion_breakpoint_in_GBA	GBAP1-like_variant_exon9-11	other_unphased_variants	input	transcript	gene	strand	coordinates(gDNA/cDNA/protein)	region	info	CHROM	POS	REF	ALT
NA20815.final	FALSE	TRUE	4	N/A	L483P/	None	GBA:L483P	NM_001005742.2 (protein_coding)	GBA	-	chr1:g.155235252A>G/c.1448T>C/p.L483P	inside_[cds_in_exon_11]	CSQN=Missense;reference_codon=CTG;candidate_codons=CCT,CCG,CCA,CCC;candidate_mnv_variants=chr1:g.155235251_155235252delCAinsAG,chr1:g.155235251_155235252delCAinsTG,chr1:g.155235251_155235252delCAinsGG;dbxref=GeneID:2629,HGNC:HGNC:4177,MIM:606463;aliases=NP_001005742;source=RefSeq	chr1	155235252	A	G

Reference

• Toffoli, M., Chen, X., Sedlazeck, F.J. et al. Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson’s disease-associated GBA gene. Commun Biol 5, 670 (2022). https://doi.org/10.1038/s42003-022-03610-7
• Zhou, W., Chen, T., Chong, Z. et al. TransVar: a multilevel variant annotator for precision genomics. Nat Methods 12, 1002–1003 (2015). https://doi.org/10.1038/nmeth.3622

Citations

If you use this tool for your analysis, please cite the gauchian-enrich as follows:

SciCrunch ID: Gauchian-enrich (RRID:SCR_027296)

Anand Maurya. (2025). maurya-anand/gauchian-enrich: v1.0.0 (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.16366908