IMPACT-SNV

Integrated Mapping of Phenotype-Associated Candidate Targets for SNV/Indel Analysis

This repository contains the IMPACT-SNV pipeline, which processes and prioritizes single nucleotide variants (SNVs) and indels for rare disease analysis using the FAVOR database and phenotype-specific gene-disease associations.

Overview

IMPACT-SNV is part of the broader IMPACT framework for phenotype-configurable interpretation of genomic variants. This module specifically handles SNV/Indel processing and produces output files compatible with IMPACT-VIS for interactive visualization and analysis.

Pipeline Architecture

The pipeline consists of four modular steps, each available as a DNAnexus applet:

VCF Files → [Step 1: Merge] → [Step 2: VCF2GDS] → [Step 3: FAVOR Annotate] → [Step 4: Prioritize] → *_SNV_IMPACT.gds

Step	Folder	Description	Input	Output
1	step1_vcf_merge/	Merges multiple VCF files into chromosome-separated files	.vcf, .vcf.gz	merged_chr*.vcf.gz
2	step2_vcf2gds/	Converts VCF to GDS format for efficient processing	.vcf.gz	merged_chr*.gds
3	step3_favorannotator-rap/	Annotates variants using FAVOR database	.gds	favor_merged_chr*.gds
4	step4_impact_prioritization/	Scores and prioritizes variants by pathogenicity	.gds, GeneList.txt	*_SNV_IMPACT.gds

Requirements

Software Dependencies

• R ≥ 4.0 with Bioconductor packages:
  • SeqArray, SeqVarTools, gdsfmt
  • stringi, dplyr, tidyr
• Python 3 (for VCF merging scripts)
• BCFtools, bgzip, tabix (for VCF processing)
• Rust and xsv (for FAVOR annotation step)

Platform

These tools are designed for deployment on the DNAnexus Research Analysis Platform. Each folder contains a dxapp.json configuration file for building DNAnexus applets.

Input Requirements

Step 1: VCF Merge

• Input: One or more VCF or VCF.GZ files
• Output: Chromosome-separated VCF.GZ files (merged_chr1.vcf.gz, merged_chr2.vcf.gz, etc.)

Step 2: VCF to GDS

• Input: VCF.GZ file from Step 1
• Output: GDS file (merged_chr*.gds)

Step 3: FAVOR Annotation

• Input: GDS file from Step 2
• Output: Annotated GDS with FAVOR functional annotations

Step 4: IMPACT Prioritization

• Input:
  • Annotated GDS files from Step 3 (merged_chr*.gds)
  • Gene-disease association file (GeneList.txt) - tab-separated with columns:
    • symbol: Gene symbol (e.g., GJB2, OTOF)
    • globalScore: Open Targets association score (0-1)
• Output: Per-sample GDS files ({sample_id}_SNV_IMPACT.gds)

Output File Format

The final *_SNV_IMPACT.gds files contain:

Core SeqArray Nodes

Node	Type	Description
variant.id	integer	Unique variant identifier
chromosome	integer/character	Chromosome
position	integer	1-based genomic position
sample.id	character	Sample identifiers
genotype	integer	Genotype array

IMPACT Score Annotations

Node	Type	Description
annotation/info/impact_score	numeric	Pathogenicity score (0-100)
annotation/info/impact_score_calc	character	Tier and calculation formula
annotation/info/tier	integer	Priority tier (1-4)

ClinVar Significance Flags

Boolean indicators under annotation/info/clnsig_flags/:

• pathogenic, likely_pathogenic, uncertain_significance
• likely_benign, benign
• pathogenic_low_penetrance, likely_pathogenic_low_penetrance
• established_risk_allele, likely_risk_allele, uncertain_risk_allele
• affects, association, drug_response, confers_sensitivity
• protective, other, conflicting_interpretations_of_pathogenicity, not_provided

FAVOR Functional Annotations

Node	Description
annotation/info/FunctionalAnnotation/VarInfo	Functional consequence
annotation/info/FunctionalAnnotation/genecode_comprehensive_info	Gene information
annotation/info/FunctionalAnnotation/clnsig	ClinVar clinical significance
annotation/info/FunctionalAnnotation/clndn	ClinVar disease name
annotation/info/FunctionalAnnotation/bravo_af	Bravo allele frequency
annotation/info/FunctionalAnnotation/apc_protein_function_v3	Protein function score

Usage

DNAnexus Platform

Step 1: VCF Merge

dx run step1_vcf_merge \
  -ivcfs=sample1.vcf.gz \
  -ivcfs=sample2.vcf.gz \
  -o merged_output

Step 2: VCF to GDS Conversion

dx run vcf2gds \
  -ivcf_file=merged_chr1.vcf.gz \
  -igds_filename=merged_chr1.gds

Step 3: Functional Annotation

dx run favorannotator \
  -igds=merged_chr1.gds \
  -ichromosome=1 \
  -iuse_compression=TRUE

Step 4: Variant Prioritization

dx run step4_impact_prioritization \
  -igenelist=GeneList.txt \
  -igds_files=favor_merged_chr1.gds \
  -igds_files=favor_merged_chr2.gds

Local Execution

For Step 4 local execution:

cd step4_impact_prioritization/resources/home/dnanexus/
Rscript IMPACT-prioritization.r --genelist GeneList.txt --outprefix anno_merged_

Integration with IMPACT-VIS

The output *_SNV_IMPACT.gds files are designed for direct use with IMPACT-VIS, an interactive R Shiny application for variant visualization.

Preparing Data for IMPACT-VIS

1. Place output files in the IMPACT-VIS app/data/ directory
2. Follow the naming convention: {sample_id}_SNV_IMPACT.gds
3. See the IMPACT-VIS Data Preparation Guide for details

IMPACT-VIS Capabilities

• Interactive visualization of prioritized variants
• Filtering by tier, ClinVar significance, allele frequency
• Gene-based and genomic region filtering
• Publication-ready plots with Plotly
• Persistent annotation states for sample curation

Tiering System

Variants are assigned to tiers based on evidence strength:

Tier	Criteria	Score Formula
Tier 1	Pathogenic/Likely Pathogenic in ClinVar + gene match	80 + 20 × globalScore
Tier 2	Frameshift, stopgain mutations	60 + 40 × globalScore
Tier 3	Nonsynonymous, nonframeshift, stoploss	20 + 80 × globalScore
Tier 4	APC protein function evidence	100 × (0.5 × APC + 0.5 × globalScore)

Gene-Disease Association File

The GeneList.txt file should contain phenotype-specific gene associations from Open Targets:

symbol	globalScore
GJB2	0.858985237
OTOF	0.850795742
MYO6	0.845566359
...

Generate this file by:

1. Querying Open Targets for your phenotype of interest
2. Exporting gene associations with global scores
3. Formatting as tab-separated with header row

References

Tools and Databases

• SeqArray - Efficient storage of sequence data
• FAVOR - Functional Annotation of Variants Online Resource
• Open Targets - Gene-disease association platform
• DNAnexus - Cloud-based genomics platform

Related IMPACT Modules

• IMPACT-VIS - Interactive visualization
• IMPACT-SV - Structural variant processing
• IMPACT-CNV - Copy number variant processing

Citation

If you use this pipeline, please cite:

@article{impact-TBA,
  title={Integrated Mapping of Phenotype-Associated Candidate Targets for 
         interpretation and prioritization of genomic variants},
  authors={Boehler, N. and Cheng, H. Y. M.},
  journal={TBA},
  year={TBA}
}

FAVOR Citation

Zhou H., et al. (2023). FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. Nucleic Acids Research, 51(D1), D1300-D1311. DOI: 10.1093/nar/gkac966

License

This project is licensed under the terms specified in the LICENSE file.

Support

• Issues: Report bugs or request features on the GitHub Issues page
• Documentation: See individual step READMEs for detailed usage
• IMPACT-VIS Help: Visit the IMPACT-VIS documentation