Colorectal cancer dataset
COVID-19 dataset of aggregated data.
This dataset contains aggregated data from 42193 individuals from COVID Population 12 Italy, Subgroup 2.
COVID-19 dataset with individual level data
This dataset contains individual level data from 42193 individuals from COVID Population 12 Italy, Subgroup 2.
COVID-19 GWAS and Allele Frequency Lookup Dataset with Population 12 (Italian) subset 1
This dataset is being used as part of the GDI Milestone 8, containing VCFs and phenotypic data in CSV format about 41514 samples. The dataset consists only of synthetic data.
COVID
COVID-19 GWAS and Allele Frequency Lookup Dataset for GDI MS 8
This is the first part of the split 11 of the synthetic data dedicated for the GDI MS8
COVID19
Smokers
National Bioinformatics Infrastructure Sweden
EOSC4Cancer Longitudinal Synthetic Colorectal Cancer Genomic data developed at BSC
The synthetic genomes have been created trying to mimic real cancer data of 4 patients (Named 185, 186, 187, and 188). Mutations are based on real CRC patients from the PCAWG dataset. For each patient, two tumor samples at different time points and one healthy sample have been simulated. The cancer intra-tumor heterogeneity and evolution in the patients is depicted by simulating reads from tumor subclones separately and then mixing them according to their clonal proportions in each sample. For rapid use and transfer, only selected chromosomes have been generated for each patient. For Beacon queries, the following url can be used https://gdi-beacon-prototype.azurewebsites.net/api/datasets/EGAD50000000276
Cancer
Colorectal Cancer
Genomics
Synthetic Data
This test dataset covers no real population.
This is test dataset
This is a description
GDI COVID 19 synthetic dataset (Population 11 Finland, Subgroup 2)
This dataset contains the pheno-clinical and genomic information of 42046 individuals from COVID Population 11 Finland, Subgroup 2. 2010 are affected by Phenotype 1, 2010 are affected by Phenotype 2, 188 are affected by Phenotype 1 and 2, and 37838 are control. The dataset also contains the information about the smoking habits of each individual.
ega
gdi
synthetic
COVID-19
SYNTHETIC Norwegian Colorectal Cancer genomic dataset generated in EOSC4Cancer
SYNTHETIC This dataset contains 10 tumor and normal pairs synthetic WGS data of colorectal cancer that were simulated in a standard format of Illumina paired-end reads. NEAT read simulator (version 3.0, https://github.com/zstephens/neat-genreads) is utilized to synthetize these 10 pairs tumor and normal WGS data. In the procedure of data generation, simulated parameters (i.e., sequencing error statistics, read fragment length distribution and GC% coverage bias) are learned from data models provided by NEAT. The average sequencing depth for tumor and normal samples aims to reach around 110X and 60X, respectively. For generation of synthetic normal WGS data per each sample, a germline variant profile from a real patient is down-sampled randomly, which includes 50% germline variants of such a patient. It is then mixed together with an in silico germline variant profile that is modelled randomly using an average mutation rate (0.001), finally constituting a full germline profile for normal synthetic WGS data. For generation of synthetic tumor WGS data per each sample, a pre-defined somatic short variant profile (SNVs+Indels) learn from a real CRC patient is added to the germline variant profile used for creating normal synthetic WGS data of the same patient, which is utilized to produce simulated sequences. Neither copy number profile nor structural variation profile is introduced into the tumor synthetic WGS data. Tumor content and ploidy are assumed to be 100% and 2.
colorectal_tumor
ngs
normal_tumor_pair
wgs
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-N_S02_L004_R2_001.fastq.gz/fastq
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-N_S02_L004_R2_001.fastq.gz in schema gdi, formatted as fastq.
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-T.bam/bam
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-T.bam in schema gdi, formatted as bam.
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-T_S04_L001_R2_001.fastq.gz/fastq
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-T_S04_L001_R2_001.fastq.gz in schema gdi, formatted as fastq.
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 22.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 22 in population 12 (ITA), sub1
Example VCF from BSC
VCF file containing GWAS and allele frequency lookup data of synthetic Colorectal cancer cases.
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 16.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 16 in population 12 (ITA), sub1
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-N.bam.bai/bai
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-N.bam.bai in schema gdi, formatted as bai.
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-N_germline_golden.vcf.gz.tbi/vcf
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-N_germline_golden.vcf.gz.tbi in schema gdi, formatted as vcf.
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-N_germline_golden.vcf.gz/vcf
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-N_germline_golden.vcf.gz in schema gdi, formatted as vcf.
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 5.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 5 in population 12 (ITA), sub1
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 11.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 11 in population 12 (ITA), sub1
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-N_S02_L002_R2_001.fastq.gz/fastq
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-N_S02_L002_R2_001.fastq.gz in schema gdi, formatted as fastq.
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 9.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 9 in population 12 (ITA), sub1
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 1.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 1 in population 12 (ITA), sub1
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-N.bam/bam
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-N.bam in schema gdi, formatted as bam.
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 12.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 12 in population 12 (ITA), sub1
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-T_S04_L003_R1_001.fastq.gz/fastq
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-T_S04_L003_R1_001.fastq.gz in schema gdi, formatted as fastq.
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-T_germline_golden.vcf.gz/vcf
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-T_germline_golden.vcf.gz in schema gdi, formatted as vcf.
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-T_germline_golden.vcf.gz.tbi/vcf
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-T_germline_golden.vcf.gz.tbi in schema gdi, formatted as vcf.
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-T_S04_L003_R2_001.fastq.gz/fastq
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-T_S04_L003_R2_001.fastq.gz in schema gdi, formatted as fastq.
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 20.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 20 in population 12 (ITA), sub1
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 15.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 15 in population 12 (ITA), sub1
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 6.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 6 in population 12 (ITA), sub1
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-N_S02_L001_R2_001.fastq.gz/fastq
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-N_S02_L001_R2_001.fastq.gz in schema gdi, formatted as fastq.
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 14.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 14 in population 12 (ITA), sub1
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 2.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 2 in population 12 (ITA), sub1
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-T_S04_L002_R1_001.fastq.gz/fastq
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-T_S04_L002_R1_001.fastq.gz in schema gdi, formatted as fastq.
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Phenotypes of the individuals.
CSV file containing phenotypes in population 12 (ITA), sub1
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 10.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 10 in population 12 (ITA), sub1
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 18.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 18 in population 12 (ITA), sub1
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 8.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 8 in population 12 (ITA), sub1
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 19.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 19 in population 12 (ITA), sub1
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration.
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-T_S04_L004_R2_001.fastq.gz/fastq
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-T_S04_L004_R2_001.fastq.gz in schema gdi, formatted as fastq.
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-T.bam.bai/bai
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-T.bam.bai in schema gdi, formatted as bai.
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 4.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 4 in population 12 (ITA), sub1
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-N_S02_L003_R2_001.fastq.gz/fastq
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-N_S02_L003_R2_001.fastq.gz in schema gdi, formatted as fastq.
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 7.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 7 in population 12 (ITA), sub1
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-N_S02_L002_R1_001.fastq.gz/fastq
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-N_S02_L002_R1_001.fastq.gz in schema gdi, formatted as fastq.
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-T_S04_L002_R2_001.fastq.gz/fastq
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-T_S04_L002_R2_001.fastq.gz in schema gdi, formatted as fastq.
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-N_S02_L001_R1_001.fastq.gz/fastq
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-N_S02_L001_R1_001.fastq.gz in schema gdi, formatted as fastq.
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-N_S02_L003_R1_001.fastq.gz/fastq
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-N_S02_L003_R1_001.fastq.gz in schema gdi, formatted as fastq.
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome X.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome X in population 12 (ITA), sub1
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 13.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 13 in population 12 (ITA), sub1
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 3.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 3 in population 12 (ITA), sub1
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-N_S02_L004_R1_001.fastq.gz/fastq
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-N_S02_L004_R1_001.fastq.gz in schema gdi, formatted as fastq.
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-T_S04_L004_R1_001.fastq.gz/fastq
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-T_S04_L004_R1_001.fastq.gz in schema gdi, formatted as fastq.
Data distribution for https://fairdata.dev.gdi.lu/api/fdp/distribution/gdi/SIM007-T_S04_L001_R1_001.fastq.gz/fastq
MOLGENIS EMX2 data distribution at https://fairdata.dev.gdi.lu for table SIM007-T_S04_L001_R1_001.fastq.gz in schema gdi, formatted as fastq.
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 21.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 21 in population 12 (ITA), sub1
GWAS and Allele Frequency Lookup Data Distribution for GDI MS8 - Population 12 (ITA), subset 1, Chromosome 17.
VCF file containing GWAS and allele frequency lookup data of synthetic COVID-19.cases and controls for GDI MS8 demonstration. VCF for chromosome 17 in population 12 (ITA), sub1