SlimCache

SlimCache is standalone tool that creates a new set of Nirvana cache files containing only transcripts from the desired transcript source.

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/SlimCache.git

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

cd SlimCache
dotnet build -c Release

Prerequisites

Using the paths to your Nirvana 3.9 or later cache and reference files, use the following command to create a new set of cache files:

Creating RefSeq-Only Cache Files

USAGE: SlimCache.dll <cache prefix> <reference path> <output cache prefix> <desired transcript source>

dotnet SlimCache.dll \
    Cache/GRCh37/Both \
    References/Homo_sapiens.GRCh37.Nirvana.dat \
    Cache/GRCh37/RefSeq \
    RefSeq

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

- loading reference sequence... finished.
- loading cache... finished.
- filtering transcripts... 196,520 transcripts removed.
- removing duplicate predictions... 101,180 predictions removed.
- writing SIFT prediction cache... finished.
- writing PolyPhen prediction cache... finished.
- writing transcript cache... finished.

Peak memory usage: 1.407 GB

Creating Ensembl-Only Cache Files

dotnet SlimCache.dll \
    Cache/GRCh37/Both \
    References/Homo_sapiens.GRCh37.Nirvana.dat \
    Cache/GRCh37/Ensembl \
    Ensembl

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

- loading reference sequence... finished.
- loading cache... finished.
- filtering transcripts... 64,624 transcripts removed.
- removing duplicate predictions... 3,438 predictions removed.
- writing SIFT prediction cache... finished.
- writing PolyPhen prediction cache... finished.
- writing transcript cache... finished.

Peak memory usage: 1.927 GB