Download Data Files
To store annotation data files, create a top-level directory. The created directory contains three subdirectories:
| • | Cache contains gene models. |
| • | SupplementaryAnnotation contains external data sources like dbSNP and gnomAD. |
| • | References contains the reference genome. |
The following command-line options are used:
|
Option |
Value |
Example |
Description |
|---|---|---|---|
|
--ga |
GRCh37, GRCh38, or both |
GRCh38 |
Genome assembly |
|
--out |
Output directory |
~/Data |
Top-level output directory |
Download data files as follows.
| 1. | To create a data directory, enter the following command. |
This example creates the Data directory in your home directory.
mkdir ~/Data
| 2. | Download the files for a genome assembly. |
This example downloads the genome assembly GRCh38.
/opt/edico/share/nirvana/Downloader --ga GRCh38 --out ~/Data
You can use the same command to resynchronize the data sources with the Illumina Annotation Engine servers, including the following actions:
| • | Remove obsolete files, such as old versions of data sources, from the output directory. |
| • | Download newer files. |
The following is the created output:
---------------------------------------------------------------------------
Downloader (c) 2020 Illumina, Inc.
Stromberg, Roy, Lajugie, Jiang, Li, and Kang 3.9.1-0-gc823805
---------------------------------------------------------------------------
- downloading manifest... 37 files.
- downloading file metadata:
- finished (00:00:00.8).
- downloading files (22.123 GB):
- downloading 1000_Genomes_Project_Phase_3_v3_plus_refMinor.rma.idx (GRCh38)
- downloading MITOMAP_20200224.nsa.idx (GRCh38)
- downloading ClinVar_20200302.nsa.idx (GRCh38)
- downloading REVEL_20160603.nsa.idx (GRCh38)
- downloading phyloP_hg38.npd.idx (GRCh38)
- downloading ClinGen_Dosage_Sensitivity_Map_20200131.nsi (GRCh38)
- downloading MITOMAP_SV_20200224.nsi (GRCh38)
- downloading dbSNP_151_globalMinor.nsa.idx (GRCh38)
- downloading ClinGen_Dosage_Sensitivity_Map_20190507.nga (GRCh38)
- downloading PrimateAI_0.2.nsa.idx (GRCh38)
- downloading ClinGen_disease_validity_curations_20191202.nga (GRCh38)
- downloading 1000_Genomes_Project_Phase_3_v3_plus.nsa.idx (GRCh38)
- downloading SpliceAi_1.3.nsa.idx (GRCh38)
- downloading dbSNP_153.nsa.idx (GRCh38)
- downloading TOPMed_freeze_5.nsa.idx (GRCh38)
- downloading MITOMAP_20200224.nsa (GRCh38)
- downloading gnomAD_2.1.nsa.idx (GRCh38)
- downloading ClinGen_20160414.nsi (GRCh38)
- downloading gnomAD_gene_scores_2.1.nga (GRCh38)
- downloading 1000_Genomes_Project_(SV)_Phase_3_v5a.nsi (GRCh38)
- downloading MultiZ100Way_20171006.pcs (GRCh38)
- downloading 1000_Genomes_Project_Phase_3_v3_plus_refMinor.rma (GRCh38)
- downloading ClinVar_20200302.nsa (GRCh38)
- downloading OMIM_20200409.nga (GRCh38)
- downloading Both.transcripts.ndb (GRCh38)
- downloading REVEL_20160603.nsa (GRCh38)
- downloading PrimateAI_0.2.nsa (GRCh38)
- downloading dbSNP_151_globalMinor.nsa (GRCh38)
- downloading Both.sift.ndb (GRCh38)
- downloading Both.polyphen.ndb (GRCh38)
- downloading Homo_sapiens.GRCh38.Nirvana.dat
- downloading 1000_Genomes_Project_Phase_3_v3_plus.nsa (GRCh38)
- downloading phyloP_hg38.npd (GRCh38)
- downloading SpliceAi_1.3.nsa (GRCh38)
- downloading TOPMed_freeze_5.nsa (GRCh38)
- downloading dbSNP_153.nsa (GRCh38)
- downloading gnomAD_2.1.nsa (GRCh38)
- finished (00:04:10.1).
Description Status
---------------------------------------------------------------------------
1000_Genomes_Project_(SV)_Phase_3_v5a.nsi (GRCh38) OK
1000_Genomes_Project_Phase_3_v3_plus.nsa (GRCh38) OK
1000_Genomes_Project_Phase_3_v3_plus.nsa.idx (GRCh38) OK
1000_Genomes_Project_Phase_3_v3_plus_refMinor.rma (GRCh38) OK
1000_Genomes_Project_Phase_3_v3_plus_refMinor.rma.idx (... OK
Both.polyphen.ndb (GRCh38) OK
Both.sift.ndb (GRCh38) OK
Both.transcripts.ndb (GRCh38) OK
ClinGen_20160414.nsi (GRCh38) OK
ClinGen_Dosage_Sensitivity_Map_20190507.nga (GRCh38) OK
ClinGen_Dosage_Sensitivity_Map_20200131.nsi (GRCh38) OK
ClinGen_disease_validity_curations_20191202.nga (GRCh38) OK
ClinVar_20200302.nsa (GRCh38) OK
ClinVar_20200302.nsa.idx (GRCh38) OK
Homo_sapiens.GRCh38.Nirvana.dat OK
MITOMAP_20200224.nsa (GRCh38) OK
MITOMAP_20200224.nsa.idx (GRCh38) OK
MITOMAP_SV_20200224.nsi (GRCh38) OK
MultiZ100Way_20171006.pcs (GRCh38) OK
OMIM_20200409.nga (GRCh38) OK
PrimateAI_0.2.nsa (GRCh38) OK
PrimateAI_0.2.nsa.idx (GRCh38) OK
REVEL_20160603.nsa (GRCh38) OK
REVEL_20160603.nsa.idx (GRCh38) OK
SpliceAi_1.3.nsa (GRCh38) OK
SpliceAi_1.3.nsa.idx (GRCh38) OK
TOPMed_freeze_5.nsa (GRCh38) OK
TOPMed_freeze_5.nsa.idx (GRCh38) OK
dbSNP_151_globalMinor.nsa (GRCh38) OK
dbSNP_151_globalMinor.nsa.idx (GRCh38) OK
dbSNP_153.nsa (GRCh38) OK
dbSNP_153.nsa.idx (GRCh38) OK
gnomAD_2.1.nsa (GRCh38) OK
gnomAD_2.1.nsa.idx (GRCh38) OK
gnomAD_gene_scores_2.1.nga (GRCh38) OK
phyloP_hg38.npd (GRCh38) OK
phyloP_hg38.npd.idx (GRCh38) OK
---------------------------------------------------------------------------
Peak memory usage: 52.3 MB
Time: 00:04:12.2
