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# 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 and Indels from a VCF/BCF of variants and SAM/BAM/CRAMs for a child and parents. In the future, it will be able to operate without the VCF/BCF of variants and perform de novo variant calling.
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.

This project is very much still in progress and should be considered an alpha release.
## Getting Started

1. Download a .jar from the [releases page](https://github.com/PankratzLab/SuperNovo/releases)
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.

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