Public Available Data
Computer Code
Public available data
We archive GWAS summary statistics made available by us or others. These included UK Biobank GWAS summary statistics (over 300 thousand individuals of European ancestory, generated by Benjamin Neale and colleagues), Pairwise Mendelian randomization results in UK Biobank (generated by us), and public available genome-wide summary statistics from published GWAS and consortia. We thank the researchers and consortia who made these valuable data available to the public.
Due to the restrictions from the computer center of Jilin University, we are not able to post the data in the internet. However, the aforementioned data could be transfered to you upon request, while the requested data shall be managerable to us.
| Dataset | Description | Update time |
|---|---|---|
| 1000G_cosmopolitan_nosingle_SNPonly.vcf.gz | 1000 Genomes multiple population genotype calls in VCF format (N=1092). | 10/2015 |
| UKBB-ID_gwas_imputed_v3_bothsexes.tsv.gz | UK Biobank GWAS summary statistics in both males and females. Array data were imputed to MRC, UK10K, 1000Genomes combined reference panel. "UKBB-ID" represents the trait ID in UKBB data showcase. | 10/2018 |
| UKBB-ID_gwas_imputed_v3_male.tsv.gz | UK Biobank GWAS summary statistics in male individuals only. | 10/2018 |
| UKBB-ID_gwas_imputed_v3_female.tsv.gz | UK Biobank GWAS summary statistics in female individuals only. | 10/2018 |
Computer code
We write scripts of various languages, including perl, R, python, to facilitate our analysis. We are happy share these code with other. These computer codes came in no warrenty.
| Script | Description | Language |
|---|---|---|
| ukbb-screening.pl | extract the summary statistics of selected SNPs from GWAS files generated by Neale lab. Tabix is required. | perl |
| MR_bonf.r | Mendelian randomization analysis using data extracted by ukbb-screening.pl. Requirement: TwoSampleMR; MRInstruments. | R |
| MR_gwas.r | Mendelian randomization analysis using gwas catalog data in MRbase. Requirement: TwoSampleMR; MRInstruments. | R |