Packages
Package	Description
DefaultPackage
db	A simple variant database backed by SQLite
gngs	All the core classes making up Groovy NGS Utils
gngs.coverage
gngs.db
gngs.gencode
gngs.pair	A set of classes supporting extraction of paired reads efficiently from BAM files
gngs.plot
gngs.plot.bx
gngs.sample
gngs.tools	Command line tools that are supported by the `gngstool` command
trie	Classes supporting efficient indexing of a large number of sequences vi prefix or suffix

Groovy NGS

Welcome to Groovy NGS!

GNGS is toolkit for working with next genomic sequencing data in Groovy.

GNGS aims unlock the power of the JVM for working with genomic data through highly accessible scripting style use.

GNGS works at three levels:

Examples of functionality supported are:

Reading, processing and filtering VCF files, including integration with common annotation sources such as VEP
Working with Genomic Ranges - full set of operation as well as higher level reading, processing and filtering
Reading, processing and performing logical operations with pedigree (PED) files and family structures
Working with BAM/SAM/CRAM files (including, generating and working with Pileups)
A range of statistical operations including R-like data frames and linear modeling constructs
Many many more useful operations