VariantQC: A Visual QC Report for Variant Evaluation

VariantQC is a standalone Java tool that generates a QC report to summarize millions of variants concisely and highlight potential problems. This tool utilizes GATK's VariantEval tool for variant evaluation and leverages MultiQC's HTML QC report.

High throughput sequencing advancements have accelerated genomic studies of human disease and these large scale sequencing studies typically produce millions of sequence variants. Because QC evaluation ensures derived genotype data is consistent and accuarte, there is a need for QC reports to summarize millions of variants concisely and to highlight potential problems. VariantQC address these needs by summarizing variant evaluation results in an interactive visual QC report.

Getting Started

Prerequisites

• Java 1.8 (How to install Java)

Installing

1. Download the jar file from here.
2. Go to the folder containing the jar file
3. Run the VariantQC command

Parameters

Argument	Default Value	Summary
-T, --analysis_type	NA	Specify 'VariantQC' tool name
-R, --reference_sequence	NA	Reference genome for VCF's species
-ped, --pedigree	NA	Pedigree file for VCF samples, only used to get gender information
-V, --variant	NA	VCF to be evaluated and summarized
-o, --out	stdout	Output

Usage Example

java -jar VariantQC.jar \
   -T VariantQC \
   -R reference.fasta \
   -ped gatk.ped \
   -V input.vcf \
   -o output.html 

Example VariantQC Report

Authors

• Benjamin N. Bimber, Ph.D.
• Melissa Yan

Acknowledgments

This work is supported by NIH grants R24 OD021324 and P51 OD011092. We wish to acknowledge the Broad Institute for permission to use the GATK toolkit and Phil Ewels for permission to use MultiQC.