https://github.com/illumina/gffcreator
Creates GFF files from Nirvana cache files
https://github.com/illumina/gffcreator
Last synced: 3 months ago
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Creates GFF files from Nirvana cache files
- Host: GitHub
- URL: https://github.com/illumina/gffcreator
- Owner: Illumina
- License: gpl-3.0
- Created: 2021-01-26T22:38:51.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2021-08-10T19:17:12.000Z (almost 4 years ago)
- Last Synced: 2025-01-24T09:27:45.895Z (5 months ago)
- Language: C#
- Size: 65.4 KB
- Stars: 0
- Watchers: 8
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# GffCreator
GffCreator is a standalone tool that creates a [GTF (GFF v2)](https://www.ensembl.org/info/website/upload/gff.html) 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](https://dotnet.microsoft.com/download/dotnet/5.0):
```
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
```
```bash
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:
```bash
- 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](https://github.com/Illumina/Nirvana/blob/v3.2.3/VariantAnnotation/Caches/DataStructures/Transcript.cs#L106-L1009). To generate a GFF file for a specific version of Nirvana, just update the Nirvana submodule accordingly.