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 .. code-block:: bash . |-- 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 .. csv-table:: :header: "Annotation","Category","File" :widths: 20,20,60 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