CloudOS data¶
You can access the 100kGP data in CloudOS. This includes the clinical data and the VCF (variant) files, but does not include the BAM/CRAM (alignment) files.
However CloudOS also contains COVID-19 data.
Summary of data availability¶
| Data programme | Type of data | Format | CloudOS availability | HPC availability |
|---|---|---|---|---|
| 100kGP clinical data | Tables | Labkey tables tsv files cohort browser |
 |
|
| 100kGP rare disease | Reads | BAM or CRAM | |
|
| 100kGP rare disease | Variants | VCF | ||
| 100kGP cancer germline | Reads | BAM or CRAM | |
|
| 100kGP cancer germline | Variants | VCF | ||
| 100kGP cancer and rare disease germline | Aggregate variants | VCF | ||
| 100kGP cancer somatic | Reads | BAM or CRAM | |
|
| 100kGP cancer somatic | Variants | VCF | ||
| 100kGP cancer somatic | Aggregate variants | VCF | ||
| GMS clinical data | Tables | Labkey tables | |
|
| GMS rare disease | Reads | BAM or CRAM | |
|
| GMS rare disease | Variants | VCF | |
|
| GMS cancer germline | Reads | BAM or CRAM | |
|
| GMS cancer germline | Variants | VCF | |
|
| GMS cancer somatic | Reads | BAM or CRAM | |
|
| GMS cancer somatic | Variants | VCF | |
|
| COVID clinical data | Tables | tsv files cohort browser |
|
|
| COVID-19 | Reads | BAM or CRAM | |
|
| COVID-19 | Variants | VCF | |
|
| COVID-19 | Aggregate variants | VCF | |
Clinical data tables¶
100kGP clinical data tables can be accessed through CloudOS with Cohort browser and flat .tsv files, which you can use with pipelines or interactively with Jupyter notebooks. The tables have been renamed compared to their names in LabKey, as listed in the table below.
| LabKey table name | Cohort Browser dataset name | File name in CloudOS |
|---|---|---|
| cancer_analysis | GEL Cancer Analysis | gel_cancer_analysis_100k.tsv |
| cancer_care_plan | GEL Cancer Care Plan | gel_cancer_care_plan_100k.tsv |
| cancer_participant_disease | GEL Cancer Disease | gel_cancer_disease_100k.tsv |
| cancer_invest_imaging | GEL Cancer Imaging | gel_cancer_imaging_100k.tsv |
| cancer_invest_sample_pathology | GEL Cancer Pathology | gel_cancer_pathology_100k.tsv |
| cancer_risk_factor_cancer_spec | GEL Cancer Risk Factor | gel_cancer_risk_factor_100k.tsv |
| cancer_risk_factor_general | GEL Cancer Risk Factor general | gel_cancer_risk_factor_general_100k.tsv |
| cancer_specific_pathology | GEL Cancer Specific Pathology | gel_cancer_specific_pathology_100k.tsv |
| cancer_surgery | GEL Cancer Surgery | gel_cancer_surgery_100k.tsv |
| cancer_participant_tumour | GEL Cancer Tumour | gel_cancer_tumour_100k.tsv |
| cancer_participant_tumour_meta | GEL Cancer Tumour Metastases | gel_cancer_tumour_metastases_100k.tsv |
| cancer_invest_circulating_tumour | GEL Circulating Tumour Marker | gel_circulating_tumour_marker_100k.tsv |
| clinic_sample | GEL Clinic Sample | gel_clinic_sample_100k.tsv |
| clinic_sample_quality_check_re | GEL Clinic Sample QC Results | gel_clinic_sample_qc_results_100k.tsv |
| denovo_cohort_information | GEL Denovo Cohort Information | gel_denovo_cohort_information_100k.tsv |
| denovo_flagged_variants | GEL Denovo Flagged Variants | gel_denovo_flagged_variants_100k.tsv |
| domain_assignment | GEL Domain Assignment | gel_domain_assignment_100k.tsv |
| cancer_100K_genomes_realigned | GEL Dragen realigned 100kGP genomes | gel_dragen_realigned_100k_genomes_100k.tsv |
| exomiser | GEL Exomiser | gel_exomiser_100k.tsv |
| gmc_exit_questionnaire | GEL Genomic Medical Centre exit questionnaire | gel_genomic_medical_centre_exit_questionnaire_100k.tsv |
| death_details | GEL Genomic Medicine Centre Death Details | gel_gmc_death_details_100k.tsv |
| laboratory_sample | GEL Laboratory Sample | gel_laboratory_sample_100k.tsv |
| laboratory_sample_omics_availa | GEL Laboratory Sample Omics | gel_laboratory_sample_omics_100k.tsv |
| lrs_laboratory_sample | GEL Long Read Sequencing Laboratory Sample | gel_lrs_laboratory_sample_100k.tsv |
| sequencing_data | GEL Long Read Sequencing Data | gel_lrs_sequencing_data_100k.tsv |
| panels_applied | GEL Panels Applied | gel_panels_applied_100k.tsv |
| participant | GEL Participant | gel_participant_100k.tsv |
| linking_table | GEL Participant ID linkage to Genome file path | GEL |
| plated_sample | GEL Plated Sample | gel_plated_sample_100k.tsv |
| rare_disease_analysis | GEL Rare Disease Analysis | gel_rare_disease_analysis_100k.tsv |
| aggregate_gvcf_sample_stats | GEL rare disease and germline genomic variant call format sample statistics | gel_rare_disease_and_germline_genomic_variant_call_format_sample_statistics_100k.tsv |
| rare_diseases_invest_blood_lab | GEL Rare Disease Blood Test Results | gel_rare_disease_blood_test_results_100k.tsv |
| rare_diseases_early_childhood | GEL Rare Disease Childhood | gel_rare_disease_childhood_100k.tsv |
| rare_diseases_family | GEL Rare Disease Family | gel_rare_disease_family_100k.tsv |
| rare_diseases_gen_measurement | GEL Rare Disease General Measurement | gel_rare_disease_general_measurement_100k.tsv |
| rare_diseases_invest_genetic | GEL Rare Disease Genetic Test | gel_rare_disease_genetic_test_100k.tsv |
| rare_diseases_invest_genetic_t | GEL Rare Disease Genetic Test Result | gel_rare_disease_genetic_test_result_100k.tsv |
| rare_diseases_imaging | GEL Rare Disease Imaging | gel_rare_disease_imaging_100k.tsv |
| rare_disease_interpreted | GEL Rare Disease Interpreted | gel_rare_disease_interpreted_100k.tsv |
| rare_diseases_participant_dise | GEL Rare Participant Disease | gel_rare_participant_disease_100k.tsv |
| rare_diseases_participant_phen | GEL Rare Participant Phenotype | gel_rare_participant_phenotype_100k.tsv |
| rare_diseases_pedigree | GEL Rare Pedigree | gel_rare_pedigree_100k.tsv |
| rare_diseases_pedigree_member | GEL Rare Pedigree Member | gel_rare_pedigree_member_100k.tsv |
| sequencing_report | GEL Sequencing Report | gel_sequencing_report_100k.tsv |
| tiered_variants_frequency | GEL Tiered Variants Frequency | gel_tiered_variants_frequency_100k.tsv |
| tiering_data | GEL Tiering Data | gel_tiering_data_100k.tsv |
| av_imd | NCRAS Cancer Index of Multiple Deprivation | ncras_cancer_index_of_multiple_deprivation_100k.tsv |
| av_patient | NCRAS Cancer Patient | ncras_cancer_patient_100k.tsv |
| av_rtd | NCRAS Cancer Route to Diagnosis | ncras_cancer_route_to_diagnosis_100k.tsv |
| av_treatment | NCRAS Cancer Treatment | ncras_cancer_treatment_100k.tsv |
| av_tumour | NCRAS Cancer Tumour | ncras_cancer_tumour_100k.tsv |
| cwt | NCRAS Cancer Waiting Times | ncras_cancer_waiting_times_100k.tsv |
| ncras_did | NCRAS Diagnostic Imaging Metadata | ncras_diagnostic_imaging_metadata_100k.tsv |
| lucada_2013 | NCRAS Lung Cancer Dataset 2013 | ncras_lung_cancer_dataset_2013_100k.tsv |
| lucada_2014 | NCRAS Lung Cancer Dataset 2014 | ncras_lung_cancer_dataset_2014_100k.tsv |
| rtds | NCRAS Radiotherapy | ncras_radiotherapy_100k.tsv |
| sact | NCRAS Systemic Anti Cancer Therapy (curated) | ncras_systemic_anti_cancer_therapy_curated_100k.tsv |
| cancer_register_nhsd | NHS D Cancer Registry | nhs_d_cancer_registry_100k.tsv |
| cen | NHS D Cohort Event Notification | nhs_d_cohort_event_notification_100k.tsv |
| did_bridge | NHS D Diagnostic Imaging Linkage | nhs_d_diagnostic_imaging_linkage_100k.tsv |
| did | NHS D Diagnostic Imaging Metadata | nhs_d_diagnostic_imaging_metadata_100k.tsv |
| ecds | NHS D Emergency Care dataset | nhs_d_emergency_care_dataset_100k.tsv |
| hes_ae | NHS D Hospital Episodes Statistics Accident and Emergency | nhs_d_hospital_episodes_statistics_accident_and_emergency_100k.tsv |
| hes_apc | NHS D Hospital Episodes Statistics Admitted Patient Care | nhs_d_hospital_episodes_statistics_admitted_patient_care_100k.tsv |
| hes_cc | NHS D Hospital Episodes Statistics Critical Care | nhs_d_hospital_episodes_statistics_critical_care_100k.tsv |
| hes_op | NHS D Hospital Episodes Statistics Outpatient | nhs_d_hospital_episodes_statistics_outpatient_100k.tsv |
| mhldds_episode | NHS D Mental Health Learning and Disability Data Set Episodes | nhs_d_mental_health_learning_and_disability_data_set_episodes_100k.tsv |
| mhldds_event | NHS D Mental Health Learning and Disability Data Set Events | nhs_d_mental_health_learning_and_disability_data_set_events_100k.tsv |
| mhldds_record | NHS D Mental Health Learning and Disability Data Set Records | nhs_d_mental_health_learning_and_disability_data_set_records_100k.tsv |
| mh_bridge | NHS D Mental Health Linkage | nhs_d_mental_health_linkage_100k.tsv |
| mhmd_v4_episode | NHS D Mental Health Minimum Dataset Episodes | nhs_d_mental_health_minimum_dataset_episodes_100k.tsv |
| mhmd_v4_event | NHS D Mental Health Minimum Dataset Events | nhs_d_mental_health_minimum_dataset_events_100k.tsv |
| mhmd_v4_record | NHS D Mental Health Minimum Dataset Records | nhs_d_mental_health_minimum_dataset_records_100k.tsv |
| proms | NHS D Patient Related Outcome Measures | nhs_d_patient_related_outcome_measures_100k.tsv |
| ons | Office of National Statistics Mortality | office_of_national_statistics_mortality_100k.tsv |
| mortality | Office of National Statistics Mortality | office_of_national_statistics_mortality_100k.tsv |
| cancer_staging_consolidated | GEL Cancer Tumour Linkage | phe_gel_cancer_tumour_linkage_100k.tsv |
| breast_specific_dataset_pilot | GEL Curated Cancer Breast | phe_gel_curated_cancer_breast_100k.tsv |
| colorectal_specific_dataset_pi | GEL Curated Cancer Colorectal | phe_gel_curated_cancer_colorectal_100k.tsv |
| glioma_specific_dataset_pilot | PGEL Curated Cancer Glioma | phe_gel_curated_cancer_glioma_100k.tsv |
| renal_specific_dataset_pilot | GEL Curated Cancer Renal | phe_gel_curated_cancer_renal_100k.tsv |
| sact_uncurated | Systemic Anti Cancer Therapy (un curated) | phe_systemic_anti_cancer_therapy_un_curated_100k.tsv |