SuperNovo

SuperNovo is a utility for identifying and validating De Novo Mutations in Next Generation Sequencing data. It's current functionality is to generate a file of metrics for De Novo SNPs from a VCF/BCF of variants and SAM/BAM/CRAMs for a child and parents.

Getting Started

1. Download a .jar from the releases page
2. Run java -jar supernovo.jar (replacing supernovo.jar with the version you downloaded) to get the help text which details the required parameters and a number of optional parameters to override default thresholds and behavior.