GffCreator

GffCreator is a standalone tool that creates a GTF (GFF v2) output file from a Nirvana transcript cache file.

Building

Remember to clone the git repo using the recursive option - this will automatically handle the Nirvana submodule:

git clone --recursive https://github.com/Illumina/GffCreator.git

After that, build the solution using the .NET 5.0 SDK:

cd GffCreator
dotnet build -c Release

Running GffCreator

Using the paths to your Nirvana 3.2.3 cache and reference files, use the following command to create the GFF file:

USAGE: GffCreator.dll <transcript source> <transcript cache path> <reference path> <output GFF path>

dotnet bin/Release/net5.0/GffCreator.dll \
	RefSeq \
	Cache/26/GRCh37/RefSeq.transcripts.ndb \
	References/6/Homo_sapiens.GRCh37.Nirvana.dat \
	GRCh37_RefSeq_26.gff.gz

When this command is run, the following output is displayed:

- loading reference sequence... finished.
- loading cache... finished.
- filter by transcript source... 101,270 remaining.
- updating transcript & gene coordinates... 1 transcripts & 1 genes updated.
- writing GFF entries... finished.

Caveats

The current version of GffCreator is using Nirvana 3.2.3 as a git submodule. As such, the GFF files produced by this tool will also contain the updated gene models that were manually added to that version. To generate a GFF file for a specific version of Nirvana, just update the Nirvana submodule accordingly.