diff --git a/beacon/connections/mongo/analyses.py b/beacon/connections/mongo/analyses.py index 63cad96..df8f186 100644 --- a/beacon/connections/mongo/analyses.py +++ b/beacon/connections/mongo/analyses.py @@ -71,7 +71,19 @@ def get_variants_of_analysis(self, entry_id: Optional[str], qparams: RequestPara schema = DefaultSchemas.GENOMICVARIATIONS return schema, 0, -1, None, dataset position=str(position) - query_cl={ position: "y", "datasetId": dataset} + filters=qparams.query.filters + if filters != []: + for filter in filters: + if filter['id']=='GENO:GENO_0000458': + query_cl={"$or": [{ position: "10", "datasetId": dataset}, { position: "01", "datasetId": dataset}]} + qparams.query.filters.remove(filter) + elif filter['id']=='GENO:GENO_0000136': + query_cl={"$or": [{ position: "11", "datasetId": dataset}]} + qparams.query.filters.remove(filter) + else: + query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]} + else: + query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]} string_of_ids = client.beacon.caseLevelData \ .find(query_cl, {"id": 1, "_id": 0}).limit(qparams.query.pagination.limit).skip(qparams.query.pagination.skip) HGVSIds=list(string_of_ids) diff --git a/beacon/connections/mongo/biosamples.py b/beacon/connections/mongo/biosamples.py index 6443440..3d1ac7a 100644 --- a/beacon/connections/mongo/biosamples.py +++ b/beacon/connections/mongo/biosamples.py @@ -66,7 +66,19 @@ def get_variants_of_biosample(self, entry_id: Optional[str], qparams: RequestPar schema = DefaultSchemas.GENOMICVARIATIONS return schema, 0, -1, None, dataset position=str(position) - query_cl={ position: "y", "datasetId": dataset} + filters=qparams.query.filters + if filters != []: + for filter in filters: + if filter['id']=='GENO:GENO_0000458': + query_cl={"$or": [{ position: "10", "datasetId": dataset}, { position: "01", "datasetId": dataset}]} + qparams.query.filters.remove(filter) + elif filter['id']=='GENO:GENO_0000136': + query_cl={"$or": [{ position: "11", "datasetId": dataset}]} + qparams.query.filters.remove(filter) + else: + query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]} + else: + query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]} string_of_ids = client.beacon.caseLevelData \ .find(query_cl, {"id": 1, "_id": 0}).limit(qparams.query.pagination.limit).skip(qparams.query.pagination.skip) HGVSIds=list(string_of_ids) diff --git a/beacon/connections/mongo/data/caseLevelData.json b/beacon/connections/mongo/data/caseLevelData.json index 1ac4197..7612982 100644 --- a/beacon/connections/mongo/data/caseLevelData.json +++ b/beacon/connections/mongo/data/caseLevelData.json @@ -1 +1 @@ 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diff --git a/beacon/connections/mongo/g_variants.py b/beacon/connections/mongo/g_variants.py index fe4c9eb..40c1b71 100644 --- a/beacon/connections/mongo/g_variants.py +++ b/beacon/connections/mongo/g_variants.py @@ -87,9 +87,27 @@ def get_biosamples_of_variant(self, entry_id: Optional[str], qparams: RequestPar list_of_targets=targets[0]["biosampleIds"] list_of_positions_strings= string_of_ids[0] biosampleIds=[] - for key, value in list_of_positions_strings.items(): - if key != 'datasetId' and key != 'id' and key != '_id': - biosampleIds.append(list_of_targets[int(key)]) + filters=qparams.query.filters + if filters != []: + for filter in filters: + if filter['id']=='GENO:GENO_0000458': + for key, value in list_of_positions_strings.items(): + if key != 'datasetId' and key != 'id' and key != '_id' and value != '11': + biosampleIds.append(list_of_targets[int(key)]) + qparams.query.filters.remove(filter) + elif filter['id']=='GENO:GENO_0000136': + for key, value in list_of_positions_strings.items(): + if key != 'datasetId' and key != 'id' and key != '_id' and value != '10' and value != '01': + biosampleIds.append(list_of_targets[int(key)]) + qparams.query.filters.remove(filter) + else: + for key, value in list_of_positions_strings.items(): + if key != 'datasetId' and key != 'id' and key != '_id': + biosampleIds.append(list_of_targets[int(key)]) + else: + for key, value in list_of_positions_strings.items(): + if key != 'datasetId' and key != 'id' and key != '_id': + biosampleIds.append(list_of_targets[int(key)]) finalids=biosampleIds try: finalids=[] @@ -138,9 +156,27 @@ def get_runs_of_variant(self, entry_id: Optional[str], qparams: RequestParams, d list_of_targets=targets[0]["biosampleIds"] list_of_positions_strings= string_of_ids[0] biosampleIds=[] - for key, value in list_of_positions_strings.items(): - if key != 'datasetId' and key != 'id' and key != '_id': - biosampleIds.append(list_of_targets[int(key)]) + filters=qparams.query.filters + if filters != []: + for filter in filters: + if filter['id']=='GENO:GENO_0000458': + for key, value in list_of_positions_strings.items(): + if key != 'datasetId' and key != 'id' and key != '_id' and value != '11': + biosampleIds.append(list_of_targets[int(key)]) + qparams.query.filters.remove(filter) + elif filter['id']=='GENO:GENO_0000136': + for key, value in list_of_positions_strings.items(): + if key != 'datasetId' and key != 'id' and key != '_id' and value != '10' and value != '01': + biosampleIds.append(list_of_targets[int(key)]) + qparams.query.filters.remove(filter) + else: + for key, value in list_of_positions_strings.items(): + if key != 'datasetId' and key != 'id' and key != '_id': + biosampleIds.append(list_of_targets[int(key)]) + else: + for key, value in list_of_positions_strings.items(): + if key != 'datasetId' and key != 'id' and key != '_id': + biosampleIds.append(list_of_targets[int(key)]) try: finalids=[] for bioid in biosampleIds: @@ -188,9 +224,27 @@ def get_analyses_of_variant(self, entry_id: Optional[str], qparams: RequestParam list_of_targets=targets[0]["biosampleIds"] list_of_positions_strings= string_of_ids[0] biosampleIds=[] - for key, value in list_of_positions_strings.items(): - if key != 'datasetId' and key != 'id' and key != '_id': - biosampleIds.append(list_of_targets[int(key)]) + filters=qparams.query.filters + if filters != []: + for filter in filters: + if filter['id']=='GENO:GENO_0000458': + for key, value in list_of_positions_strings.items(): + if key != 'datasetId' and key != 'id' and key != '_id' and value != '11': + biosampleIds.append(list_of_targets[int(key)]) + qparams.query.filters.remove(filter) + elif filter['id']=='GENO:GENO_0000136': + for key, value in list_of_positions_strings.items(): + if key != 'datasetId' and key != 'id' and key != '_id' and value != '10' and value != '01': + biosampleIds.append(list_of_targets[int(key)]) + qparams.query.filters.remove(filter) + else: + for key, value in list_of_positions_strings.items(): + if key != 'datasetId' and key != 'id' and key != '_id': + biosampleIds.append(list_of_targets[int(key)]) + else: + for key, value in list_of_positions_strings.items(): + if key != 'datasetId' and key != 'id' and key != '_id': + biosampleIds.append(list_of_targets[int(key)]) try: finalids=[] for bioid in biosampleIds: @@ -238,9 +292,27 @@ def get_individuals_of_variant(self, entry_id: Optional[str], qparams: RequestPa list_of_targets=targets[0]["biosampleIds"] list_of_positions_strings= string_of_ids[0] biosampleIds=[] - for key, value in list_of_positions_strings.items(): - if key != 'datasetId' and key != 'id' and key != '_id': - biosampleIds.append(list_of_targets[int(key)]) + filters=qparams.query.filters + if filters != []: + for filter in filters: + if filter['id']=='GENO:GENO_0000458': + for key, value in list_of_positions_strings.items(): + if key != 'datasetId' and key != 'id' and key != '_id' and value != '11': + biosampleIds.append(list_of_targets[int(key)]) + qparams.query.filters.remove(filter) + elif filter['id']=='GENO:GENO_0000136': + for key, value in list_of_positions_strings.items(): + if key != 'datasetId' and key != 'id' and key != '_id' and value != '10' and value != '01': + biosampleIds.append(list_of_targets[int(key)]) + qparams.query.filters.remove(filter) + else: + for key, value in list_of_positions_strings.items(): + if key != 'datasetId' and key != 'id' and key != '_id': + biosampleIds.append(list_of_targets[int(key)]) + else: + for key, value in list_of_positions_strings.items(): + if key != 'datasetId' and key != 'id' and key != '_id': + biosampleIds.append(list_of_targets[int(key)]) try: finalquery={} finalquery["$or"]=[] diff --git a/beacon/connections/mongo/individuals.py b/beacon/connections/mongo/individuals.py index 90020bb..e429fb7 100644 --- a/beacon/connections/mongo/individuals.py +++ b/beacon/connections/mongo/individuals.py @@ -66,7 +66,19 @@ def get_variants_of_individual(self, entry_id: Optional[str], qparams: RequestPa schema = DefaultSchemas.GENOMICVARIATIONS return schema, 0, -1, None, dataset position=str(position) - query_cl={ position: "y", "datasetId": dataset} + filters=qparams.query.filters + if filters != []: + for filter in filters: + if filter['id']=='GENO:GENO_0000458': + query_cl={"$or": [{ position: "10", "datasetId": dataset}, { position: "01", "datasetId": dataset}]} + qparams.query.filters.remove(filter) + elif filter['id']=='GENO:GENO_0000136': + query_cl={"$or": [{ position: "11", "datasetId": dataset}]} + qparams.query.filters.remove(filter) + else: + query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]} + else: + query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]} string_of_ids = client.beacon.caseLevelData \ .find(query_cl, {"id": 1, "_id": 0}).limit(qparams.query.pagination.limit).skip(qparams.query.pagination.skip) HGVSIds=list(string_of_ids) diff --git a/beacon/connections/mongo/runs.py b/beacon/connections/mongo/runs.py index 43352fa..8261d10 100644 --- a/beacon/connections/mongo/runs.py +++ b/beacon/connections/mongo/runs.py @@ -67,7 +67,19 @@ def get_variants_of_run(self, entry_id: Optional[str], qparams: RequestParams, d schema = DefaultSchemas.GENOMICVARIATIONS return schema, 0, -1, None, dataset position=str(position) - query_cl={ position: "y", "datasetId": dataset} + filters=qparams.query.filters + if filters != []: + for filter in filters: + if filter['id']=='GENO:GENO_0000458': + query_cl={"$or": [{ position: "10", "datasetId": dataset}, { position: "01", "datasetId": dataset}]} + qparams.query.filters.remove(filter) + elif filter['id']=='GENO:GENO_0000136': + query_cl={"$or": [{ position: "11", "datasetId": dataset}]} + qparams.query.filters.remove(filter) + else: + query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]} + else: + query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]} string_of_ids = client.beacon.caseLevelData \ .find(query_cl, {"id": 1, "_id": 0}).limit(qparams.query.pagination.limit).skip(qparams.query.pagination.skip) HGVSIds=list(string_of_ids) diff --git a/docker-compose.yml b/docker-compose.yml index cb9270a..126eabd 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -79,6 +79,9 @@ services: volumes: - ./beacon/connections/mongo/mongo-init/:/docker-entrypoint-initdb.d/:ro - ./beacon/connections/mongo/data/:/data + - ./beacon/connections/mongo/data/db:/data/db + - ./beacon/connections/mongo/data/configdb:/data/configdb + - ./beacon/connections/mongo/data/caseLevelData:/data/caseLevelData networks: - pub #command: --verbose diff --git a/ri-tools/conf/conf.py b/ri-tools/conf/conf.py index e357d01..9785ef1 100644 --- a/ri-tools/conf/conf.py +++ b/ri-tools/conf/conf.py @@ -4,11 +4,12 @@ #### VCF Conversion config parameters #### allele_frequency=1 # introduce float number, leave 1 if you want to convert all the variants -reference_genome='GRCh37' # Choose one between NCBI36, GRCh37, GRCh38 +reference_genome='GRCh38' # Choose one between NCBI36, GRCh37, GRCh38 datasetId='CINECA_synthetic_cohort_EUROPE_UK1' case_level_data=True num_rows=7000000 population='Finnish' +zygosity=True ### MongoDB parameters ### database_host = 'mongo' diff --git a/ri-tools/output_docs/CINECA_synthetic_cohort_EUROPE_UK1/analyses.json b/ri-tools/output_docs/CINECA_synthetic_cohort_EUROPE_UK1/analyses.json index 5089975..2b5eac8 100644 --- a/ri-tools/output_docs/CINECA_synthetic_cohort_EUROPE_UK1/analyses.json +++ b/ri-tools/output_docs/CINECA_synthetic_cohort_EUROPE_UK1/analyses.json @@ -1 +1,30050 @@ -[{"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00096", "id": "UK1_analysisId_1", "individualId": "HG00096", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000001", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00097", "id": "UK1_analysisId_2", "individualId": "HG00097", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000002", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00099", "id": "UK1_analysisId_3", "individualId": "HG00099", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000003", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00100", "id": "UK1_analysisId_4", "individualId": "HG00100", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000004", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00101", "id": "UK1_analysisId_5", "individualId": "HG00101", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000005", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00102", "id": "UK1_analysisId_6", "individualId": "HG00102", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000006", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00103", "id": "UK1_analysisId_7", "individualId": "HG00103", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000007", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00105", "id": "UK1_analysisId_8", "individualId": "HG00105", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000008", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00106", "id": "UK1_analysisId_9", "individualId": "HG00106", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000009", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00107", "id": "UK1_analysisId_10", "individualId": "HG00107", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000010", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00108", "id": "UK1_analysisId_11", "individualId": "HG00108", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000011", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00109", "id": "UK1_analysisId_12", "individualId": "HG00109", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000012", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00110", "id": "UK1_analysisId_13", "individualId": "HG00110", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000013", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00111", "id": "UK1_analysisId_14", "individualId": "HG00111", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000014", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00112", "id": "UK1_analysisId_15", "individualId": "HG00112", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000015", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00113", "id": "UK1_analysisId_16", "individualId": "HG00113", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000016", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00114", "id": "UK1_analysisId_17", "individualId": "HG00114", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000017", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00115", "id": "UK1_analysisId_18", "individualId": "HG00115", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000018", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00116", "id": "UK1_analysisId_19", "individualId": "HG00116", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000019", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00117", "id": "UK1_analysisId_20", "individualId": "HG00117", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000020", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00118", "id": "UK1_analysisId_21", "individualId": "HG00118", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000021", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00119", "id": "UK1_analysisId_22", "individualId": "HG00119", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000022", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00120", "id": "UK1_analysisId_23", "individualId": "HG00120", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000023", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00121", "id": "UK1_analysisId_24", "individualId": "HG00121", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000024", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00122", "id": "UK1_analysisId_25", "individualId": "HG00122", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000025", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00123", "id": "UK1_analysisId_26", "individualId": "HG00123", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000026", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00125", "id": "UK1_analysisId_27", "individualId": "HG00125", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000027", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00126", "id": "UK1_analysisId_28", "individualId": "HG00126", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000028", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00127", "id": "UK1_analysisId_29", "individualId": "HG00127", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000029", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00128", "id": "UK1_analysisId_30", "individualId": "HG00128", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000030", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00129", "id": "UK1_analysisId_31", "individualId": "HG00129", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000031", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00130", "id": "UK1_analysisId_32", "individualId": "HG00130", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000032", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00131", "id": "UK1_analysisId_33", "individualId": "HG00131", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000033", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00132", "id": "UK1_analysisId_34", "individualId": "HG00132", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000034", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00133", "id": "UK1_analysisId_35", "individualId": "HG00133", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000035", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00136", "id": "UK1_analysisId_36", "individualId": "HG00136", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000036", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00137", "id": "UK1_analysisId_37", "individualId": "HG00137", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000037", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00138", "id": "UK1_analysisId_38", "individualId": "HG00138", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000038", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00139", "id": "UK1_analysisId_39", "individualId": "HG00139", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000039", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00140", "id": "UK1_analysisId_40", "individualId": "HG00140", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000040", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00141", "id": "UK1_analysisId_41", "individualId": "HG00141", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000041", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00142", "id": "UK1_analysisId_42", "individualId": "HG00142", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000042", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00143", "id": "UK1_analysisId_43", "individualId": "HG00143", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000043", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00145", "id": "UK1_analysisId_44", "individualId": "HG00145", "pipelineName": "1000G-low-coverage-WGS", "pipelineRef": "https://www.nature.com/articles/nature15393", "runId": "SRR00000044", "variantCaller": "GATK4.0"}, {"aligner": "bwa-0.5.9", "analysisDate": "2015-09-30", "biosampleId": "HG00146", "id": "UK1_analysisId_45", "individualId": "HG00146", 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