Getting Started
Illumina Connected Annotations is written in C# using .NET Core (an amazing runtime environment that currently runs on Windows, Linux, Mac OS X, and in Docker images). Once .NET Core has been downloaded, all you need to do is grab the source, compile it, and grab the data files.
tip
Illumina Connected Annotations currently uses .NET6.0. Please make sure that you have the most current runtime from the .NET Core downloads page.
info
Please read Prerequisite section to generate necessary credential file to run Illumina Connector Annotations.
Getting Illumina Connected Annotations
Latest Release
Please visit Illumina Connected Annotations to obtain the latest release. Download and place the zip file in the IlluminaConnectedAnnotations folder.
mkdir -p IlluminaConnectedAnnotations/Data
cd IlluminaConnectedAnnotations
unzip IlluminaConnectedAnnotations-3.25.0-0-g101034c3-net6.0.zip
Quick Start
If you want to get started right away, we've created a script that unzips the Illumina Connected Annotations build, downloads the annotation data, and starts annotating a test file:
bash ./TestIlluminaConnectedAnnotations.sh IlluminaConnectedAnnotationsBuild.zip
We have verified that this script works on Windows (using Git Bash or WSL), Linux, and Mac OS X.
Docker
Obtain the docker image in a zip file (e.g. IlluminaConnectedAnnotations-3.25.0-0-g101034c3-net6.0-docker.tar.gz), and load it as follows
docker load < IlluminaConnectedAnnotations-3.25.0-0-g101034c3-net6.0-docker.tar.gz
If you want to build your own docker image, it is really easy to do. You just need to have Illumina Connected Annotations zip file and then download the Dockerfile and this script.
Put both files (create_docker_image.sh and Dockerfile) inside the same folder.
In terminal, execute command below inside the folder where you put those scripts:
chmod +x create_docker_image.sh
./create_docker_image.sh [path to zip file] [image tag]
After you run the script, the docker image will be available in your local machine with image name illumina-connected-annotations:[image tag specified].
We have special instructions for running IlluminaConnectedAnnotations (Here's a toy VCF in case you need it):
docker run --rm -it -v local/data/folder:/scratch illumina-connected-annotations:v3.25.0 Annotator -c /scratch/Cache/ \
-r /scratch/References/Homo_sapiens.GRCh37.Nirvana.dat \
--sd /scratch/SupplementaryAnnotation/GRCh37 \
-i /scratch/HiSeq.10000.vcf.gz -o /scratch/HiSeq
caution
Please note that since our data files are usually accessed through a Docker volume, there is a noticeable performance penalty when running Illumina Connected Annotations in Docker.
tip
For convenience, the user is encouraged to create aliases for the docker commands. For example:
alias IlluminaConnectedAnnotations="docker run --rm -it -v local/data/folder:/scratch illumina-connected-annotations:v3.25.0 IlluminaConnectedAnnotations"
Downloading the data files
Check Prerequisite for more details on creating Illumina API key to use Illumina Connected Annotation and its utilities.
To download the latest data sources (or update the ones that you already have), use the following command to automate the download from S3:
dotnet DataManager.dll make-config -r GRCh37
dotnet DataManager.dll download \
-r GRCh37 \
--dir Data
Check Data Manager for more details on controlling data sources and their versions.
Glitches in the Matrix
Every once in a while, the download process does not go smoothly. Perhaps the internet connection cut out or you ran out of disk space. The DataManager attempts to detect these
situations by checking the file sizes at the very end. If you see that a file was marked truncated, try fixing the root cause and running the DataManager again.
tip
From time to time, you can re-run the DataManager to get the latest annotation files. It will only download the files that changed.
Download a test VCF file
Here's a toy VCF file you can play around with:
curl -O https://illumina.github.io/IlluminaConnectedAnnotationsDocumentation/files/HiSeq.10000.vcf.gz
Running Illumina Connected Annotations
Once you have downloaded the data sets, use the following command to annotate your VCF:
dotnet Annotator.dll \
-c Data/Cache \
--sd Data/SupplementaryAnnotation/GRCh37 \
-r Data/References/Homo_sapiens.GRCh37.Nirvana.dat \
-i HiSeq.10000.vcf.gz \
-o HiSeq.10000
- the
-cargument specifies the cache directory - the
--sdargument specifies the supplementary annotation directory - the
-rargument specifies the compressed reference path - the
-iargument specifies the input VCF path - the
-oargument specifies the output filename prefix
When running Illumina Connected Annotations, performance metrics are shown as it evaluates each chromosome in the input VCF file:
---------------------------------------------------------------------------
Illumina Connected Annotations (c) 2024 Illumina, Inc.
3.25.0
---------------------------------------------------------------------------
Initialization Time Positions/s
---------------------------------------------------------------------------
Cache 00:00:00.0
SA Position Scan 00:00:00.0 153,634
Reference Preload Annotation Variants/s
---------------------------------------------------------------------------
chr1 00:00:00.2 00:00:00.8 11,873
Summary Time Percent
---------------------------------------------------------------------------
Initialization 00:00:00.0 1.5 %
Preload 00:00:00.2 4.9 %
Annotation 00:00:00.8 18.5 %
Time: 00:00:04.4
The output will be a JSON file called HiSeq.10000.json.gz. Here's the full JSON file.
The Illumina Connected Annotations command line
The full command line options can be viewed by using the -h option or no options
dotnet Annotator.dll
---------------------------------------------------------------------------
Illumina Connected Annotations (c) 2024 Illumina, Inc.
3.25.0
---------------------------------------------------------------------------
USAGE: dotnet Annotator.dll -i <vcf path> -c <cache dir> --sd <sa dir> -r <ref path> -o <base output filename>
Annotates a set of variants
OPTIONS:
--cache, -c <directory>
input cache directory
--in, -i <path> input VCF path
--tsv <path> input VCF path
--out, -o <file path> output file path
--ref, -r <path> input compressed reference sequence path
--sd <directory> input supplementary annotation directory
--sources, -s <VALUE> annotation data sources to be used (comma
separated list of supported tags)
--credentials-file, -l <VALUE>
File path to user credentials, default is set to ~
/.ilmnAnnotations/credentials.json
--versions-config <assembly>
Annotation version config file. By default, it
will use file ~/.ilmnAnnotation/assembly_
annotation_config.json
--ignore-license-error ignore error due to invalid license and skip
related data sources
--force-mt forces to annotate mitochondrial variants
--legacy-vids enables support for legacy VIDs
--enable-dq report DQ from VCF samples field
--enable-bidirectional-fusions
enables support for bidirectional gene fusions
--disable-junction-preservation
disable junction preserving functional annotation
--str <VALUE> user provided STR annotation TSV file
--vcf-info <VALUE> additional vcf info field keys (comma separated)
desired in the output
--vcf-sample-info <VALUE>
additional vcf format field keys (comma separated)
desired in the output
--sa-cutoff <VALUE> Any SV larger than or equal to this value will
not have any supplementary annotations
--simple-nomenclature-cutoff-length <VALUE>
Any SV larger than or equal to this value will
not have any simple nomenclature annotation.
Default is 1000.
--output-format <VALUE>
output file format, available options: json, vcf.
--help, -h displays the help menu
--version, -v displays the version
##### Supported Annotation Sources #####
Basic Tier: DECIPHER, GME, GERP, DANN, REVEL, ClinGen, gnomAD, phyloP, TOPMed, DGV, 1000 Genomes, CliinVar, dbSNP, FusionCatcher, MITOMAP, MultiZ100Way
Professional Tier: PrimateAI(GRCh37), PrimateAI-3D(GRCh38), SpliceAI, COSMIC, OMIM.
##### Contact #####
Professional content licensing, feedback and technical support: annotation_support@illumina.com.
Specifying annotation sources
By default, Illumina Connected Annotations will use all available data sources. However, the user can customize the set of sources with their versions using the --versions-config
option.
An Example of versions config json file below:
{
"Ensembl":
{
"GeneModels": "110"
},
"GenomeAssembly":
{
"GenomeAssembly": "GRCh37.p13"
},
"HGNC":
{
"GeneModels": "20240603"
},
"RefSeq":
{
"GeneModels": "105.20220307"
},
"clinvar":
{
"SmallVariant": "99999999"
},
"gnomad":
{
"LowComplexityRegions": "2.1",
"SmallVariant": "2.1"
}
}
If an unknown source is specified, a warning message will be printed.
dotnet Annotator.dll \
-c Data/Cache/GRCh37 \
--sd Data/SupplementaryAnnotation/GRCh37 \
-r Data/References/Homo_sapiens.GRCh37.Nirvana.dat \
-i HiSeq.10000.vcf.gz \
-o HiSeq.10000 \
--versions-config /Users/bob/.ilmnAnnotations/customised_GRCh37_annotation_config.json
---------------------------------------------------------------------------
Illumina Connected Annotations (c) 2024 Illumina, Inc.
3.25.0
---------------------------------------------------------------------------
Some requested data sources are not loaded.
Data Source Type Status Comments
---------------------------------------------------------------------------
GenomeAssembly GenomeAssembly Loaded GRCh37.p13
RefSeq GeneModels Loaded 105.20220307
Ensembl GeneModels Loaded 110
HGNC GeneModels Loaded 20240603
gnomad SmallVariant Loaded 2.1
gnomad LowComplexityRegions Loaded 2.1
clinvar SmallVariant Skipped Version 99999999 not available
Initialization Time Positions/s
---------------------------------------------------------------------------
SA Position Scan 00:00:00.3 307,966
....
..
The list of available values is compiled from the files provided (using -c and --sd options).