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/record/5636209

greendb_query tool

The greendb query tool only need the GREEN-DB SQlite file (.db.gz) available from https://zenodo.org/record/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/record/3956385/files/GRCh37_CADD.tsv.gz
GRCh37_CADD	scores	https://zenodo.org/record/3956385/files/GRCh37_CADD.tsv.gz.csi
GRCh37_DANN	scores	https://zenodo.org/record/3957486/files/GRCh37_DANN.tsv.gz
GRCh37_DANN	scores	https://zenodo.org/record/3957486/files/GRCh37_DANN.tsv.gz.csi
GRCh37_ExPECTO	scores	https://zenodo.org/record/3956168/files/GRCh37_ExPECTO.tsv.gz
GRCh37_ExPECTO	scores	https://zenodo.org/record/3956168/files/GRCh37_ExPECTO.tsv.gz.csi
GRCh37_FIRE	scores	https://zenodo.org/record/3957356/files/GRCh37_FIRE.tsv.gz
GRCh37_FIRE	scores	https://zenodo.org/record/3957356/files/GRCh37_FIRE.tsv.gz.csi
GRCh37_LinSight	scores	https://zenodo.org/record/3956168/files/GRCh37_LinSight.bed.gz
GRCh37_LinSight	scores	https://zenodo.org/record/3956168/files/GRCh37_LinSight.bed.gz.csi
GRCh37_NCBoost	scores	https://zenodo.org/record/3956168/files/GRCh37_NCBoost.tsv.gz
GRCh37_NCBoost	scores	https://zenodo.org/record/3956168/files/GRCh37_NCBoost.tsv.gz.csi
GRCh37_ReMM	scores	https://zenodo.org/record/3956168/files/GRCh37_ReMM.tsv.gz
GRCh37_ReMM	scores	https://zenodo.org/record/3956168/files/GRCh37_ReMM.tsv.gz.csi
GRCh37_PhyloP100	scores	https://zenodo.org/record/3973181/files/GRCh37_PhyloP100.bed.gz
GRCh37_PhyloP100	scores	https://zenodo.org/record/3973181/files/GRCh37_PhyloP100.bed.gz.csi
GRCh37_Eigen	scores	https://zenodo.org/record/3982095/files/GRCh37_Eigen.tsv.gz
GRCh37_Eigen	scores	https://zenodo.org/record/3982095/files/GRCh37_Eigen.tsv.gz.csi
GRCh37_FATHMM_XF	scores	https://zenodo.org/record/3982392/files/GRCh37_FATHMM-XF_NC.tsv.gz
GRCh37_FATHMM_XF	scores	https://zenodo.org/record/3982392/files/GRCh37_FATHMM-XF_NC.tsv.gz.csi
GRCh37_FATHMM_MKL	scores	https://zenodo.org/record/3981113/files/GRCh37_FATHMM-MKL_NC.tsv.gz
GRCh37_FATHMM_MKL	scores	https://zenodo.org/record/3981113/files/GRCh37_FATHMM-MKL_NC.tsv.gz.csi
GRCh37_GWAVA	scores	https://zenodo.org/record/3956168/files/GRCh37_gwava.bed.gz
GRCh37_GWAVA	scores	https://zenodo.org/record/3956168/files/GRCh37_gwava.bed.gz.csi
GRCh37_gnomAD	AF	https://zenodo.org/record/3957637/files/GRCh37_gnomad.genomes.vcf.gz
GRCh37_gnomAD	AF	https://zenodo.org/record/3957637/files/GRCh37_gnomad.genomes.vcf.gz.csi
GRCh37_ncER	scores	https://zenodo.org/record/5636163/files/GRCh37_ncER_perc.bed.gz
GRCh37_ncER	scores	https://zenodo.org/record/5636163/files/GRCh37_ncER_perc.bed.gz.csi
GRCh38_CADD	scores	https://zenodo.org/record/3956227/files/GRCh38_CADD.tsv.gz
GRCh38_CADD	scores	https://zenodo.org/record/3956227/files/GRCh38_CADD.tsv.gz.csi
GRCh38_DANN	scores	https://zenodo.org/record/3957428/files/GRCh38_DANN.tsv.gz
GRCh38_DANN	scores	https://zenodo.org/record/3957428/files/GRCh38_DANN.tsv.gz.csi
GRCh38_ExPECTO	scores	https://zenodo.org/record/3955933/files/GRCh38_ExPECTO.tsv.gz
GRCh38_ExPECTO	scores	https://zenodo.org/record/3955933/files/GRCh38_ExPECTO.tsv.gz.csi
GRCh38_FIRE	scores	https://zenodo.org/record/3957216/files/GRCh38_FIRE.tsv.gz
GRCh38_FIRE	scores	https://zenodo.org/record/3957216/files/GRCh38_FIRE.tsv.gz.csi
GRCh38_LinSight	scores	https://zenodo.org/record/3955933/files/GRCh38_LinSight.bed.gz
GRCh38_LinSight	scores	https://zenodo.org/record/3955933/files/GRCh38_LinSight.bed.gz.csi
GRCh38_NCBoost	scores	https://zenodo.org/record/3955933/files/GRCh38_NCBoost.tsv.gz
GRCh38_NCBoost	scores	https://zenodo.org/record/3955933/files/GRCh38_NCBoost.tsv.gz.csi
GRCh38_ReMM	scores	https://zenodo.org/record/3955933/files/GRCh38_ReMM.tsv.gz
GRCh38_ReMM	scores	https://zenodo.org/record/3955933/files/GRCh38_ReMM.tsv.gz.csi
GRCh38_PhyloP100	scores	https://zenodo.org/record/3973181/files/GRCh38_PhyloP100.bed.gz
GRCh38_PhyloP100	scores	https://zenodo.org/record/3973181/files/GRCh38_PhyloP100.bed.gz.csi
GRCh38_Eigen	scores	https://zenodo.org/record/3982182/files/GRCh38_Eigen.tsv.gz
GRCh38_Eigen	scores	https://zenodo.org/record/3982182/files/GRCh38_Eigen.tsv.gz.csi
GRCh38_FATHMM_XF	scores	https://zenodo.org/record/3982484/files/GRCh38_FATHMM-XF_NC.tsv.gz
GRCh38_FATHMM_XF	scores	https://zenodo.org/record/3982484/files/GRCh38_FATHMM-XF_NC.tsv.gz.csi
GRCh38_FATHMM_MKL	scores	https://zenodo.org/record/3981121/files/GRCh38_FATHMM-MKL_NC.tsv.gz
GRCh38_FATHMM_MKL	scores	https://zenodo.org/record/3981121/files/GRCh38_FATHMM-MKL_NC.tsv.gz.csi
GRCh38_GWAVA	scores	https://zenodo.org/record/3955933/files/GRCh38_gwava.bed.gz
GRCh38_GWAVA	scores	https://zenodo.org/record/3955933/files/GRCh38_gwava.bed.gz.csi
GRCh38_ncER	scores	https://zenodo.org/record/5636163/files/GRCh38_ncER_perc.bed.gz
GRCh38_ncER	scores	https://zenodo.org/record/5636163/files/GRCh38_ncER_perc.bed.gz.csi
GRCh37_TFBS	regions	https://zenodo.org/record/5705936/files/GRCh37_TFBS.merged.bed.gz
GRCh37_TFBS	regions	https://zenodo.org/record/5705936/files/GRCh37_TFBS.merged.bed.gz.csi
GRCh37_DNase	regions	https://zenodo.org/record/5705936/files/GRCh37_DNase.merged.bed.gz
GRCh37_DNase	regions	https://zenodo.org/record/5705936/files/GRCh37_DNase.merged.bed.gz.csi
GRCh37_UCNE	regions	https://zenodo.org/record/5705936/files/GRCh37_UCNE.bed.gz
GRCh37_UCNE	regions	https://zenodo.org/record/5705936/files/GRCh37_UCNE.bed.gz.csi
GRCh37_dbSuper	regions	https://zenodo.org/record/5705936/files/GRCh37_dbSuper.bed.gz
GRCh37_dbSuper	regions	https://zenodo.org/record/5705936/files/GGRCh37_dbSuper.bed.gz.csi
GRCh37_TAD	regions	https://zenodo.org/record/5705936/files/GRCh37_TAD.bed.gz
GRCh37_TAD	regions	https://zenodo.org/record/5705936/files/GRCh37_TAD.bed.gz.csi
GRCh38_TFBS	regions	https://zenodo.org/record/5705936/files/GRCh38_TFBS.merged.bed.gz
GRCh38_TFBS	regions	https://zenodo.org/record/5705936/files/GRCh38_TFBS.merged.bed.gz.csi
GRCh38_DNase	regions	https://zenodo.org/record/5705936/files/GRCh38_DNase.merged.bed.gz
GRCh38_DNase	regions	https://zenodo.org/record/5705936/files/GRCh38_DNase.merged.bed.gz.csi
GRCh38_UCNE	regions	https://zenodo.org/record/5705936/files/GRCh38_UCNE.bed.gz
GRCh38_UCNE	regions	https://zenodo.org/record/5705936/files/GRCh38_UCNE.bed.gz.csi
GRCh38_dbSuper	regions	https://zenodo.org/record/5705936/files/GRCh38_dbSuper.bed.gz
GRCh38_dbSuper	regions	https://zenodo.org/record/5705936/files/GRCh38_dbSuper.bed.gz.csi
GRCh38_TAD	regions	https://zenodo.org/record/5705936/files/GRCh38_TAD.bed.gz
GRCh38_TAD	regions	https://zenodo.org/record/5705936/files/GRCh38_TAD.bed.gz.csi
GRCh38_gnomAD	AF	https://zenodo.org/record/3957637/files/GRCh38_gnomad.genomes.vcf.gz
GRCh38_gnomAD	AF	https://zenodo.org/record/3957637/files/GRCh38_gnomad.genomes.vcf.gz.csi
SV_annotations	SV_annotations	https://zenodo.org/record/3970785/files/SV_annotations.tar.gz
GRCh37_GREENDB_bed	GREENDB_bed	https://zenodo.org/record/5636209/files/GRCh37_GREEN-DB.bed.gz
GRCh37_GREENDB_bed	GREENDB_bed	https://zenodo.org/record/5636209/files/GRCh37_GREEN-DB.bed.gz.csi
GRCh38_GREENDB_bed	GREENDB_bed	https://zenodo.org/record/5636209/files/GRCh38_GREEN-DB.bed.gz
GRCh38_GREENDB_bed	GREENDB_bed	https://zenodo.org/record/5636209/files/GRCh38_GREEN-DB.bed.gz.csi
GREENDB_sqlite	GREENDB_sqlite	https://zenodo.org/record/5636209/files/GREEN-DB_v2.5.db.gz