G2P config for VEP backup

vcf_config.json.backup

+{
+  "collections": [
+    {
+      "id": "1000genomes_phase3_GRCh37",
+      "species": "homo_sapiens",
+      "assembly": "GRCh37",
+      "type": "remote",
+      "strict_name_match": 1,
+      "filename_template": "ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh37/variation_genotype/ALL.chr###CHR###.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y"
+      ],
+      "sample_prefix": "1000GENOMES:phase_3:"
+    },
+    {
+      "id": "1000genomes_phase3_GRCh38",
+      "species": "homo_sapiens",
+      "assembly": "GRCh38",
+      "type": "remote",
+      "strict_name_match": 1,
+      "filename_template": "ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/ALL.chr###CHR###_GRCh38.genotypes.20170504.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y"
+      ],
+      "sample_prefix": "1000GENOMES:phase_3:"
+    },
+    {
+      "id": "gnomADg_GRCh37",
+      "description": "Genome Aggregation Database genomes r2.1",
+      "species": "homo_sapiens",
+      "assembly": "GRCh37",
+      "type": "remote",
+      "filename_template": "ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh37/variation_genotype/gnomad/r2.1/genomes/gnomad.genomes.r2.1.sites.chr###CHR###_noVEP.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "20", "21", "22", "X"
+      ],
+      "population_prefix": "gnomADg:",
+      "population_display_group": {
+        "display_group_name": "gnomAD genomes",
+        "display_group_priority": 1.5
+      },
+      "populations": {
+        "9900000": {
+          "name": "gnomADg:ALL",
+          "_raw_name": "",
+          "description": "All gnomAD genomes individuals"
+        },
+        "9900001": {
+          "name": "afr",
+          "description": "African/African American"
+        },
+        "9900002": {
+          "name": "amr",
+          "description": "Latino"
+        },
+        "9900003": {
+          "name": "asj",
+          "description": "Ashkenazi Jewish"
+        },
+        "9900004": {
+          "name": "eas",
+          "description": "East Asian"
+        },
+        "9900005": {
+          "name": "fin",
+          "description": "Finnish"
+        },
+        "9900006": {
+          "name": "nfe",
+          "description": "Non-Finnish European"
+        },
+        "9900007": {
+          "name": "oth",
+          "description": "Other"
+        }
+      }
+    },
+    {
+      "id": "gnomADe_GRCh37",
+      "description": "Genome Aggregation Database exomes r2.1",
+      "species": "homo_sapiens",
+      "assembly": "GRCh37",
+      "type": "remote",
+      "filename_template": "ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh37/variation_genotype/gnomad/r2.1/exomes/gnomad.exomes.r2.1.sites.chr###CHR###_noVEP.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y"
+      ],
+      "population_prefix": "gnomADe:",
+      "population_display_group": {
+        "display_group_name": "gnomAD exomes",
+        "display_group_priority": 1.4
+      },
+      "populations": {
+        "9900010": {
+          "name": "gnomADe:ALL",
+          "_raw_name": "",
+          "description": "All gnomAD exomes individuals"
+        },
+        "9900011": {
+          "name": "afr",
+          "description": "African/African American"
+        },
+        "9900012": {
+          "name": "amr",
+          "description": "Latino"
+        },
+        "9900013": {
+          "name": "asj",
+          "description": "Ashkenazi Jewish"
+        },
+        "9900014": {
+          "name": "eas",
+          "description": "East Asian"
+        },
+        "9900015": {
+          "name": "fin",
+          "description": "Finnish"
+        },
+        "9900016": {
+          "name": "nfe",
+          "description": "Non-Finnish European"
+        },
+        "9900017": {
+          "name": "oth",
+          "description": "Other"
+        },
+        "9900018": {
+          "name": "sas",
+          "description": "South Asian"
+        }
+      }
+    },
+    {
+      "id": "gnomADg_r3.0_GRCh38",
+      "description": "Genome Aggregation Database genomes r3.0",
+      "species": "homo_sapiens",
+      "assembly": "GRCh38",
+      "type": "local",
+      "filename_template": "/home/u035/project/resources/gnomad/r3.0/genomes/gnomad.genomes.r3.0.sites.chr###CHR###_trimmed_info.vcf.bgz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y"
+      ],
+      "use_seq_region_synonyms": 1,
+      "population_prefix": "gnomADg:",
+      "population_display_group": {
+        "display_group_name": "gnomAD genomes",
+        "display_group_priority": 1.6
+      },
+      "populations": {
+        "9900028": {
+          "name": "gnomADg:ALL",
+          "_raw_name": "",
+          "description": "All gnomAD genomes individuals"
+        },
+        "9900029": {
+          "name": "afr",
+          "description": "African/African American"
+        },
+        "9900030": {
+          "name": "ami",
+          "description": "Amish"
+        },
+        "9900031": {
+          "name": "amr",
+          "description": "Latino/Admixed American"
+        },
+        "9900032": {
+          "name": "asj",
+          "description": "Ashkenazi Jewish"
+        },
+        "9900033": {
+          "name": "eas",
+          "description": "East Asian"
+        },
+        "9900034": {
+          "name": "fin",
+          "description": "Finnish"
+        },
+        "9900035": {
+          "name": "nfe",
+          "description": "Non-Finnish European"
+        },
+        "9900036": {
+          "name": "sas",
+          "description": "South Asian"
+        },
+        "9900037": {
+          "name": "oth",
+          "description": "Other"
+        }
+      }
+    },
+    {
+      "id": "gnomADe_GRCh38",
+      "description": "Genome Aggregation Database exomes r2.1",
+      "species": "homo_sapiens",
+      "assembly": "GRCh38",
+      "type": "local",
+      "filename_template": "/home/u035/project/resources/gnomad/r2.1/exomes/gnomad.exomes.r2.1.sites.grch38.chr###CHR###_noVEP.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y"
+      ],
+      "population_prefix": "gnomADe:",
+      "population_display_group": {
+        "display_group_name": "gnomAD exomes",
+        "display_group_priority": 1.4
+      },
+      "populations": {
+        "9900010": {
+          "name": "gnomADe:ALL",
+          "_raw_name": "",
+          "description": "All gnomAD exomes individuals"
+        },
+        "9900011": {
+          "name": "afr",
+          "description": "African/African American"
+        },
+        "9900012": {
+          "name": "amr",
+          "description": "Latino"
+        },
+        "9900013": {
+          "name": "asj",
+          "description": "Ashkenazi Jewish"
+        },
+        "9900014": {
+          "name": "eas",
+          "description": "East Asian"
+        },
+        "9900015": {
+          "name": "fin",
+          "description": "Finnish"
+        },
+        "9900016": {
+          "name": "nfe",
+          "description": "Non-Finnish European"
+        },
+        "9900017": {
+          "name": "oth",
+          "description": "Other"
+        },
+        "9900018": {
+          "name": "sas",
+          "description": "South Asian"
+        }
+      }
+    },
+    {
+      "id": "topmed_GRCh37",
+      "species": "homo_sapiens",
+      "assembly": "GRCh37",
+      "type": "remote",
+      "filename_template": "ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh37/variation_genotype/TOPMED_GRCh37.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y"
+      ],
+      "source_name": "TOPMed",
+      "population_display_group": {
+        "display_group_name": "TOPMed",
+        "display_group_priority": 2.5
+      },
+      "populations": {
+        "9990000": {
+          "name": "TOPMed",
+          "_raw_name": "TOPMed",
+          "_af": "TOPMED",
+          "description": "Trans-Omics for Precision Medicine (TOPMed) Program"
+        }
+      }
+    },
+    {
+      "id": "topmed_GRCh38",
+      "species": "homo_sapiens",
+      "assembly": "GRCh38",
+      "type": "remote",
+      "filename_template": "ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/TOPMED_GRCh38_20180418.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y"
+      ],
+      "source_name": "TOPMed",
+      "population_display_group": {
+        "display_group_name": "TOPMed",
+        "display_group_priority": 2.5
+      },
+      "populations": {
+        "9990000": {
+          "name": "TOPMed",
+          "_raw_name": "TOPMed",
+          "_af": "TOPMED",
+          "description": "Trans-Omics for Precision Medicine (TOPMed) Program"
+        }
+      }
+    },
+    {
+      "id": "uk10k_GRCh37",
+      "species": "homo_sapiens",
+      "assembly": "GRCh37",
+      "type": "remote",
+      "filename_template": "ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh37/variation_genotype/UK10K_COHORT.20160215.sites.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y"
+      ],
+      "source_name": "UK10K",
+      "population_prefix": "UK10K:",
+      "population_display_group": {
+        "display_group_name": "UK10K",
+        "display_group_priority": 2.6
+      },
+      "populations": {
+        "9999000": {
+          "name": "ALSPAC",
+          "_raw_name": "ALSPAC",
+          "description": "ALSPAC cohort"
+        },
+        "9999001": {
+          "name": "TWINSUK",
+          "_raw_name": "TWINSUK_NODUP",
+          "description": "TWINSUK cohort excluding 67 samples where a monozygotic or dyzygotic twin was included in the release"
+        }
+      }
+    },
+    {
+      "id": "uk10k_GRCh38",
+      "species": "homo_sapiens",
+      "assembly": "GRCh38",
+      "type": "remote",
+      "filename_template": "ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/UK10K_COHORT.20160215.sites.GRCh38.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y"
+      ],
+      "source_name": "UK10K",
+      "population_prefix": "UK10K:",
+      "population_display_group": {
+        "display_group_name": "UK10K",
+        "display_group_priority": 2.6
+      },
+      "populations": {
+        "9999000": {
+          "name": "ALSPAC",
+          "_raw_name": "ALSPAC",
+          "description": "ALSPAC cohort"
+        },
+        "9999001": {
+          "name": "TWINSUK",
+          "_raw_name": "TWINSUK_NODUP",
+          "description": "TWINSUK cohort excluding 67 samples where a monozygotic or dyzygotic twin was included in the release"
+        }
+      }
+    },
+    { "id": "esp_GRCh37",
+      "species": "homo_sapiens",
+      "assembly": "GRCh37",
+      "type": "remote",
+      "filename_template": "ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh37/variation_genotype/ESP6500SI-V2-SSA137.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y"
+      ],
+      "source_name": "NHLBI Exome Sequencing Project",
+      "population_display_group": {
+        "display_group_name": "NHLBI Exome Sequencing Project",
+        "display_group_priority": 2.7
+      },
+      "population_prefix": "ESP6500:",
+      "populations": {
+        "9910000": {
+          "name": "AA",
+          "description": "African American",
+          "_ac": "AA_AC"
+        },
+        "9910001": {
+          "name": "EA",
+          "description": "European American",
+          "_ac": "EA_AC"
+        }
+      }
+    },
+    { "id": "esp_GRCh38",
+      "species": "homo_sapiens",
+      "assembly": "GRCh38",
+      "type": "remote",
+      "filename_template": "ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/ESP6500SI-V2-SSA137_GRCh38.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y"
+      ],
+      "source_name": "NHLBI Exome Sequencing Project",
+      "population_display_group": {
+        "display_group_name": "NHLBI Exome Sequencing Project",
+        "display_group_priority": 2.7
+      },
+      "population_prefix": "ESP6500:",
+      "populations": {
+        "9910000": {
+          "name": "AA",
+          "description": "African American",
+          "_ac": "AA_AC"
+        },
+        "9910001": {
+          "name": "EA",
+          "description": "European American",
+          "_ac": "EA_AC"
+        }
+      }
+    },
+    {
+      "id": "nextgen_cow_irbt",
+      "species": "bos_taurus",
+      "assembly": "ARS-UCD1.2",
+      "type": "remote",
+      "filename_template": "ftp://ftp.ensembl.org/pub/data_files/bos_taurus/ARS-UCD1.2/variation_genotype/IRBT_ARS-UCD1_2.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "28", "29", "X"
+      ],
+      "population_prefix": "NextGen:"
+    },
+    {
+      "id": "nextgen_sheep_iroa",
+      "species": "ovis_aries",
+      "assembly": "Oar_v3.1",
+      "type": "remote",
+      "filename_template": "ftp://ftp.ensembl.org/pub/data_files/ovis_aries/Oar_v3.1/variation_genotype/IROA.population_sites.OARv3_1.20140307.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "X"
+      ],
+      "population_prefix": "NextGen:"
+    },
+    {
+      "id": "nextgen_sheep_mooa",
+      "species": "ovis_aries",
+      "assembly": "Oar_v3.1",
+      "type": "remote",
+      "filename_template": "ftp://ftp.ensembl.org/pub/data_files/ovis_aries/Oar_v3.1/variation_genotype/MOOA.population_sites.OARv3_1.20140328.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "X"
+      ],
+      "population_prefix": "NextGen:"
+    },
+    {
+      "id": "sheep_genome_consortium",
+      "species": "ovis_aries",
+      "assembly": "Oar_v3.1",
+      "type": "remote",
+      "filename_template" : "ftp://ftp.ensembl.org/pub/data_files/ovis_aries/Oar_v3.1/variation_genotype/###CHR###.filtered_intersect.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "X", "MT"
+      ],
+      "population_prefix": "ISGC:",
+      "sample_prefix": "ISGC:"
+    },
+    {
+      "id": "nextgen_goat",
+      "species": "capra_hircus",
+      "assembly": "ARS1",
+      "type": "remote",
+      "filename_template" : "ftp://ftp.ensembl.org/pub/data_files/capra_hircus/ARS1/variation_genotype/NextGenCapraHircusRemappedARS1.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "28", "29"
+      ],
+      "population_prefix": "NextGen:",
+      "sample_prefix": "NextGen:"
+    },
+    {
+      "id": "mouse_genome_project_snp",
+      "species": "mus_musculus",
+      "assembly": "GRCm38",
+      "type": "remote",
+      "filename_template": "ftp://ftp.ensembl.org/pub/data_files/mus_musculus/GRCm38/variation_genotype/mgp.v3.snps.sorted.rsIDdbSNPv137.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "X", "Y"
+      ],
+      "sample_prefix": "MGP:"
+    },
+    {
+      "id": "mouse_genome_project_indel",
+      "species": "mus_musculus",
+      "assembly": "GRCm38",
+      "type": "remote",
+      "filename_template": "ftp://ftp.ensembl.org/pub/data_files/mus_musculus/GRCm38/variation_genotype/mgp.v3.indels.sorted.rsIDdbSNPv137.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",
+        "15", "16", "17", "18", "19", "X", "Y"
+      ],
+      "sample_prefix": "MGP:"
+    },
+    {
+      "id": "dog_EVA_PRJEB24066",
+      "species": "canis_familiaris",
+      "assembly": "CanFam3.1",
+      "type": "remote",
+      "filename_template" : "ftp://ftp.ebi.ac.uk/pub/databases/eva/PRJEB24066/dogs.557.publicSamples.ann.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21",
+        "22", "23", "24", "25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "X", "MT"
+      ],
+      "sample_prefix": "PRJEB24066:"
+    },
+    {
+      "id": "horse_EVA_PRJEB9799",
+      "species": "equus_caballus",
+      "assembly": "EquCab3.0",
+      "type": "remote",
+      "filename_template" : "ftp://ftp.ensembl.org/pub/data_files/equus_caballus/EquCab3.0/variation_genotype/PRJEB9799_EquCab3_0.vcf.gz",
+      "chromosomes": [
+        "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21",
+        "22", "23", "24", "25", "26", "27", "28", "29", "30", "31", "X", "MT"
+      ],
+      "sample_prefix": "PRJEB9799:"
+    },
+    {
+      "id": "atlantic_salmon_EVA_PRJEB34225",
+      "source_name": "PRJEB34225",
+      "description": "Variants from EVA study PRJEB34225",
+      "species": "salmo_salar",
+      "assembly": "ICSASG_v2",
+      "type": "remote",
+      "use_as_source" : 1,
+      "use_seq_region_synonyms": 1,
+      "strict_name_match" : 0,
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+}