Download resources

greenvaran tool

The greenvaran annotation tool only need the GREEN-DB BED file and index for your genome build available from https://zenodo.org/records/5636209

greendb_query tool

The greendb query tool only need the GREEN-DB SQlite file (.db.gz) available from https://zenodo.org/records/5636209 Remember to decompress this before use

GREEN-VARAN workflow

To perform annotations GREEN-VARAN Nextflow workflow requires a series of supporting files. By default, various resources are expected in the resources folder within the main tool folder. If you pass an alternative resource folder using --resource_folder option, the same structure is expected in this folder The expected folder structure is as follows and the expected file names are those listed in the Zenodo repository table below

.
|-- SQlite
|   `-- GREEN-DB_v2.5.db
|-- GRCh37
|   `-- BED / TSV files used for GRCh37 genome build
`-- GRCh38
    `-- BED / TSV files used for GRCh38 genome build

When you clone the GREEN-VARAN repository you can use the Nextflow workflow workflow/download.nf to download files and prepare the resource folder. Use the --list_data option to see the full list of available resource and the expected path for each one.

Otherwise, single files are available for download from Zenodo repository

Annotation

Category

File

GRCh37_CADD

scores

https://zenodo.org/records/3956385/files/GRCh37_CADD.tsv.gz

GRCh37_CADD

scores

https://zenodo.org/records/3956385/files/GRCh37_CADD.tsv.gz.csi

GRCh37_DANN

scores

https://zenodo.org/records/3957486/files/GRCh37_DANN.tsv.gz

GRCh37_DANN

scores

https://zenodo.org/records/3957486/files/GRCh37_DANN.tsv.gz.csi

GRCh37_ExPECTO

scores

https://zenodo.org/records/3956168/files/GRCh37_ExPECTO.tsv.gz

GRCh37_ExPECTO

scores

https://zenodo.org/records/3956168/files/GRCh37_ExPECTO.tsv.gz.csi

GRCh37_FIRE

scores

https://zenodo.org/records/3957356/files/GRCh37_FIRE.tsv.gz

GRCh37_FIRE

scores

https://zenodo.org/records/3957356/files/GRCh37_FIRE.tsv.gz.csi

GRCh37_LinSight

scores

https://zenodo.org/records/3956168/files/GRCh37_LinSight.bed.gz

GRCh37_LinSight

scores

https://zenodo.org/records/3956168/files/GRCh37_LinSight.bed.gz.csi

GRCh37_NCBoost

scores

https://zenodo.org/records/3956168/files/GRCh37_NCBoost.tsv.gz

GRCh37_NCBoost

scores

https://zenodo.org/records/3956168/files/GRCh37_NCBoost.tsv.gz.csi

GRCh37_ReMM

scores

https://zenodo.org/records/3956168/files/GRCh37_ReMM.tsv.gz

GRCh37_ReMM

scores

https://zenodo.org/records/3956168/files/GRCh37_ReMM.tsv.gz.csi

GRCh37_PhyloP100

scores

https://zenodo.org/records/3973181/files/GRCh37_PhyloP100.bed.gz

GRCh37_PhyloP100

scores

https://zenodo.org/records/3973181/files/GRCh37_PhyloP100.bed.gz.csi

GRCh37_Eigen

scores

https://zenodo.org/records/3982095/files/GRCh37_Eigen.tsv.gz

GRCh37_Eigen

scores

https://zenodo.org/records/3982095/files/GRCh37_Eigen.tsv.gz.csi

GRCh37_FATHMM_XF

scores

https://zenodo.org/records/3982392/files/GRCh37_FATHMM-XF_NC.tsv.gz

GRCh37_FATHMM_XF

scores

https://zenodo.org/records/3982392/files/GRCh37_FATHMM-XF_NC.tsv.gz.csi

GRCh37_FATHMM_MKL

scores

https://zenodo.org/records/3981113/files/GRCh37_FATHMM-MKL_NC.tsv.gz

GRCh37_FATHMM_MKL

scores

https://zenodo.org/records/3981113/files/GRCh37_FATHMM-MKL_NC.tsv.gz.csi

GRCh37_GWAVA

scores

https://zenodo.org/records/3956168/files/GRCh37_gwava.bed.gz

GRCh37_GWAVA

scores

https://zenodo.org/records/3956168/files/GRCh37_gwava.bed.gz.csi

GRCh37_gnomAD

AF

https://zenodo.org/records/3957637/files/GRCh37_gnomad.genomes.vcf.gz

GRCh37_gnomAD

AF

https://zenodo.org/records/3957637/files/GRCh37_gnomad.genomes.vcf.gz.csi

GRCh37_ncER

scores

https://zenodo.org/records/5636163/files/GRCh37_ncER_perc.bed.gz

GRCh37_ncER

scores

https://zenodo.org/records/5636163/files/GRCh37_ncER_perc.bed.gz.csi

GRCh38_CADD

scores

https://zenodo.org/records/3956227/files/GRCh38_CADD.tsv.gz

GRCh38_CADD

scores

https://zenodo.org/records/3956227/files/GRCh38_CADD.tsv.gz.csi

GRCh38_DANN

scores

https://zenodo.org/records/3957428/files/GRCh38_DANN.tsv.gz

GRCh38_DANN

scores

https://zenodo.org/records/3957428/files/GRCh38_DANN.tsv.gz.csi

GRCh38_ExPECTO

scores

https://zenodo.org/records/3955933/files/GRCh38_ExPECTO.tsv.gz

GRCh38_ExPECTO

scores

https://zenodo.org/records/3955933/files/GRCh38_ExPECTO.tsv.gz.csi

GRCh38_FIRE

scores

https://zenodo.org/records/3957216/files/GRCh38_FIRE.tsv.gz

GRCh38_FIRE

scores

https://zenodo.org/records/3957216/files/GRCh38_FIRE.tsv.gz.csi

GRCh38_LinSight

scores

https://zenodo.org/records/3955933/files/GRCh38_LinSight.bed.gz

GRCh38_LinSight

scores

https://zenodo.org/records/3955933/files/GRCh38_LinSight.bed.gz.csi

GRCh38_NCBoost

scores

https://zenodo.org/records/3955933/files/GRCh38_NCBoost.tsv.gz

GRCh38_NCBoost

scores

https://zenodo.org/records/3955933/files/GRCh38_NCBoost.tsv.gz.csi

GRCh38_ReMM

scores

https://zenodo.org/records/3955933/files/GRCh38_ReMM.tsv.gz

GRCh38_ReMM

scores

https://zenodo.org/records/3955933/files/GRCh38_ReMM.tsv.gz.csi

GRCh38_PhyloP100

scores

https://zenodo.org/records/3973181/files/GRCh38_PhyloP100.bed.gz

GRCh38_PhyloP100

scores

https://zenodo.org/records/3973181/files/GRCh38_PhyloP100.bed.gz.csi

GRCh38_Eigen

scores

https://zenodo.org/records/3982182/files/GRCh38_Eigen.tsv.gz

GRCh38_Eigen

scores

https://zenodo.org/records/3982182/files/GRCh38_Eigen.tsv.gz.csi

GRCh38_FATHMM_XF

scores

https://zenodo.org/records/3982484/files/GRCh38_FATHMM-XF_NC.tsv.gz

GRCh38_FATHMM_XF

scores

https://zenodo.org/records/3982484/files/GRCh38_FATHMM-XF_NC.tsv.gz.csi

GRCh38_FATHMM_MKL

scores

https://zenodo.org/records/3981121/files/GRCh38_FATHMM-MKL_NC.tsv.gz

GRCh38_FATHMM_MKL

scores

https://zenodo.org/records/3981121/files/GRCh38_FATHMM-MKL_NC.tsv.gz.csi

GRCh38_GWAVA

scores

https://zenodo.org/records/3955933/files/GRCh38_gwava.bed.gz

GRCh38_GWAVA

scores

https://zenodo.org/records/3955933/files/GRCh38_gwava.bed.gz.csi

GRCh38_ncER

scores

https://zenodo.org/records/5636163/files/GRCh38_ncER_perc.bed.gz

GRCh38_ncER

scores

https://zenodo.org/records/5636163/files/GRCh38_ncER_perc.bed.gz.csi

GRCh37_TFBS

regions

https://zenodo.org/records/5705936/files/GRCh37_TFBS.merged.bed.gz

GRCh37_TFBS

regions

https://zenodo.org/records/5705936/files/GRCh37_TFBS.merged.bed.gz.csi

GRCh37_DNase

regions

https://zenodo.org/records/5705936/files/GRCh37_DNase.merged.bed.gz

GRCh37_DNase

regions

https://zenodo.org/records/5705936/files/GRCh37_DNase.merged.bed.gz.csi

GRCh37_UCNE

regions

https://zenodo.org/records/5705936/files/GRCh37_UCNE.bed.gz

GRCh37_UCNE

regions

https://zenodo.org/records/5705936/files/GRCh37_UCNE.bed.gz.csi

GRCh37_dbSuper

regions

https://zenodo.org/records/5705936/files/GRCh37_dbSuper.bed.gz

GRCh37_dbSuper

regions

https://zenodo.org/records/5705936/files/GRCh37_dbSuper.bed.gz.csi

GRCh37_TAD

regions

https://zenodo.org/records/5705936/files/GRCh37_TADs.bed.gz

GRCh37_TAD

regions

https://zenodo.org/records/5705936/files/GRCh37_TADs.bed.gz.tbi

GRCh38_TFBS

regions

https://zenodo.org/records/5705936/files/GRCh38_TFBS.merged.bed.gz

GRCh38_TFBS

regions

https://zenodo.org/records/5705936/files/GRCh38_TFBS.merged.bed.gz.csi

GRCh38_DNase

regions

https://zenodo.org/records/5705936/files/GRCh38_DNase.merged.bed.gz

GRCh38_DNase

regions

https://zenodo.org/records/5705936/files/GRCh38_DNase.merged.bed.gz.csi

GRCh38_UCNE

regions

https://zenodo.org/records/5705936/files/GRCh38_UCNE.bed.gz

GRCh38_UCNE

regions

https://zenodo.org/records/5705936/files/GRCh38_UCNE.bed.gz.csi

GRCh38_dbSuper

regions

https://zenodo.org/records/5705936/files/GRCh38_dbSuper.bed.gz

GRCh38_dbSuper

regions

https://zenodo.org/records/5705936/files/GRCh38_dbSuper.bed.gz.csi

GRCh38_TAD

regions

https://zenodo.org/records/5705936/files/GRCh38_TADs.bed.gz

GRCh38_TAD

regions

https://zenodo.org/records/5705936/files/GRCh38_TADs.bed.gz.tbi

GRCh38_gnomAD

AF

https://zenodo.org/records/3957637/files/GRCh38_gnomad.genomes.vcf.gz

GRCh38_gnomAD

AF

https://zenodo.org/records/3957637/files/GRCh38_gnomad.genomes.vcf.gz.csi

SV_annotations

SV_annotations

https://zenodo.org/records/3970785/files/SV_annotations.tar.gz

GRCh37_GREENDB_bed

GREENDB_bed

https://zenodo.org/records/5636209/files/GRCh37_GREEN-DB.bed.gz

GRCh37_GREENDB_bed

GREENDB_bed

https://zenodo.org/records/5636209/files/GRCh37_GREEN-DB.bed.gz.csi

GRCh38_GREENDB_bed

GREENDB_bed

https://zenodo.org/records/5636209/files/GRCh38_GREEN-DB.bed.gz

GRCh38_GREENDB_bed

GREENDB_bed

https://zenodo.org/records/5636209/files/GRCh38_GREEN-DB.bed.gz.csi

GREENDB_sqlite

GREENDB_sqlite

https://zenodo.org/records/5636209/files/GREEN-DB_v2.5.db.gz