Commands: discover

This command uses the reads passed to genotype and the personalised reference genome it produced to discover new variants, using Cortex, an assembly-based variant caller.

The variants discovered get rebased, ie expressed in terms of the VCF from genotype. This means you can run gramtools build using the original VCF and the one from this command, to augment the original graph with the newly found variation.

Usage

gramtools discover -i ./run -o ./discover

parameter	description
-i	Output directory from genotype
-o	Output directory for this command