Input Specifications Overview

Introduction to IMPACT-VIS input data formats and validation

Authors

Affiliation

Nicholas Boehler

University of Toronto Mississauga

Hai-Ying Mary Cheng

University of Toronto Mississauga

1 File Formats Supported

IMPACT-VIS accepts three types of genomic variant data:

Data Type	Format	File Suffix	Size	Required?
SNV/Indel	GDS (Binary)	.gds	500 MB typical	Yes
Structural Variants	AnnotSV TSV	.tsv	2-5 MB typical	No
Copy Number Variants	Tab-separated TXT	.txt	5-10 MB typical	No

2 Organization

All data must be placed in app/data/ with this structure:

app/data/
├── sample001_SNV_IMPACT.gds
├── sample001_SNV_IMPACT.gds_variant_states.rds
├── sample001_SV_IMPACT.tsv
├── sample001_CNV_IMPACT.txt
├── sample002_SNV_IMPACT.gds
├── sample002_SNV_IMPACT.gds_variant_states.rds
├── sample002_SV_IMPACT.tsv
└── sample002_CNV_IMPACT.txt

3 Quick Validation

Before loading data, verify:

# Check files exist and are readable
ls -lh app/data/sample001*

# Verify GDS is valid (in R)
library(SeqArray)
gds <- seqOpen("app/data/sample001_SNV_IMPACT.gds")
seqClose(gds)  # Should complete without error

# Verify TSV/TXT format
head -5 app/data/sample001_SV_IMPACT.tsv
head -5 app/data/sample001_CNV_IMPACT.txt

4 Detailed Format Documentation

For complete format specifications, see:

• GDS Format — Genomic Data Structure schema
• SV Format — AnnotSV TSV structure
• CNV Format — Copy number variant format
• Test Fixtures — Example files

5 Next Steps

1. Preparing data? → See Data Preparation Guide
2. Need GDS format? → See GDS Format
3. Creating from VCF? → See Data Preparation
4. Ready to load? → See Quick Start

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Document Version: 1.0.0
Last Updated: 2025-12-17