From f24de2089860a9cb7356d64a7aa08c22151a0100 Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Fri, 18 Jun 2021 11:40:01 +0100
Subject: [PATCH] G2P config for VEP backup
---
vcf_config.json.backup | 737 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 737 insertions(+)
create mode 100644 vcf_config.json.backup
diff --git a/vcf_config.json.backup b/vcf_config.json.backup
new file mode 100644
index 0000000..fc5941c
--- /dev/null
+++ b/vcf_config.json.backup
@@ -0,0 +1,737 @@
+{
+ "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,
+ "filename_template" : "ftp://ftp.ebi.ac.uk/pub/databases/eva/PRJEB34225/Salmon_SNP_80_samples_freebayes_EBI_noINFO.vcf.gz",
+ "chromosomes": [
+ "ssa01", "ssa02", "ssa03", "ssa04", "ssa05", "ssa06", "ssa07", "ssa08", "ssa09", "ssa10", "ssa11", "ssa12", "ssa13", "ssa14", "ssa15", "ssa16", "ssa17", "ssa18", "ssa19", "ssa20", "ssa21", "ssa22", "ssa23", "ssa24", "ssa25", "ssa26", "ssa27", "ssa28", "ssa29"
+ ]
+ },
+ {
+ "id": "vervet_EVA_PRJEB22989",
+ "source_name": "PRJEB22989",
+ "species": "chlorocebus_sabaeus",
+ "assembly": "ChlSab1.1",
+ "type": "remote",
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+}
--
GitLab