hg38 gerpScore database?

[hurrialice]

Hi Nirvana team,

Thanks for building this nice tool. I would like to GERP++ annotation for my hg38 VCF. However when I download the data source with

dotnet bin/Downloader.dll --ga GRCh38 -o Data

I don't find the GERP bed file of interest in Data/:

../../Nirvana/Data/
├── Cache
│   └── GRCh38
│       ├── Both.polyphen.ndb
│       ├── Both.sift.ndb
│       └── Both.transcripts.ndb
├── References
│   └── Homo_sapiens.GRCh38.Nirvana.dat
└── SupplementaryAnnotation
    └── GRCh38
        ├── 1000_Genomes_Project_Phase_3_v3_plus.nsa
        ├── 1000_Genomes_Project_Phase_3_v3_plus.nsa.idx
        ├── 1000_Genomes_Project_Phase_3_v3_plus_refMinor.rma
        ├── 1000_Genomes_Project_Phase_3_v3_plus_refMinor.rma.idx
        ├── 1000_Genomes_Project_(SV)_Phase_3_v5a.nsi
        ├── ClinGen_20160414.nsi
        ├── ClinGen_disease_validity_curations_20211201.nga
        ├── ClinGen_Dosage_Sensitivity_Map_20211201.nga
        ├── ClinGen_Dosage_Sensitivity_Map_20211201.nsi
        ├── ClinVar_20211202.nsa
        ├── ClinVar_20211202.nsa.idx
        ├── dbSNP_151_globalMinor.nsa
        ├── dbSNP_151_globalMinor.nsa.idx
        ├── dbSNP_154.nsa
        ├── dbSNP_154.nsa.idx
        ├── FusionCatcher_1.33.gfs
        ├── gnomAD_3.1.nsa
        ├── gnomAD_3.1.nsa.idx
        ├── gnomAD_gene_scores_2.1.nga
        ├── gnomAD_LCR_2.1.lcr
        ├── MITOMAP_20200819.nsa
        ├── MITOMAP_20200819.nsa.idx
        ├── MITOMAP_SV_20200819.nsi
        ├── MultiZ100Way_20171006.pcs
        ├── OMIM_20211202.nga
        ├── phyloP_hg38.npd
        ├── phyloP_hg38.npd.idx
        ├── PrimateAI_0.2.nsa
        ├── PrimateAI_0.2.nsa.idx
        ├── REVEL_20200205.nsa
        ├── REVEL_20200205.nsa.idx
        ├── SpliceAi_1.3.nsa
        ├── SpliceAi_1.3.nsa.idx
        ├── TOPMed_freeze_5.nsa
        └── TOPMed_freeze_5.nsa.idx

and hence no gerpScore key in the output JSON at any level. Did I miss something obvious?

FYI I work at Illumina and can access ussd-rnd cluster -- if there is the GERP++ annotation data source available somewhere on shared disk please let me know!

Thanks!

[rajatshuvro]

Issue has been fixed in the 3.18.1 release.

[hurrialice]

Hi @rajatshuvro,

Thanks but I did not find Downloader.dll in https://github.com/Illumina/Nirvana/releases/download/v3.18.1/Nirvana-3.18.1-net6.0.zip. Can you confirm if it's included in the v3.18.1 release?

I also tried to dotnet build from source but encountered many errors like:

/illumina/thirdparty/dotnet/6.0.200/sdk/6.0.200/NuGet.targets(564,5): error : Unable to obtain lock file access on
 '/tmp/NuGetScratch/lock/07417655d07d48671cf7288a6b81fd3e79011411' for operations on 
'/home/qzhang9/.nuget/NuGet/NuGet.Config'. This may mean that a different user or administrator is holding this lock and
 that this process does not have permission to access it. If no other process is currently performing an operation on this 
file it may mean that an earlier NuGet process crashed and left an inaccessible lock file, in this case removing the file 
'/tmp/NuGetScratch/lock/07417655d07d48671cf7288a6b81fd3e79011411' will allow NuGet to continue. [/illumina-
isi07/scratch/iResolve/qz/annotation/Nirvana/VariantAnnotation.Interface/VariantAnnotation.Interface.csproj]

Any clues? Thanks!

[rajatshuvro]

You are correct @hurrialice about missing Downloader.dll from the zip. I will fix that soon. About the build error, it seems to be a permission issue on your machine. Please work with your sys admin.

[Cataliarubio]

Hi, Nirvana team i am using Nirvanna annotations, and iI would like to GERP++ annotation for my hg38 VCF. So in my Cache files is this Gerp_20110522.gsa but it no gerpScore in the output JSON are. so i appreciate your help thanks