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2. Tutorial
The directory SAFFARI/resources/ includes example files you can use to test running the fine-mapping pipeline.
The file Mullins_2021_loci_ranges.tsv contains example summary statistics from GWAS whilst the top loci file Mullins_2021_toploci.csv contains the top GWAS loci with genome-wide significance (P < 5 × 10−8).
Make sure to also download
(i) the baseline-LF2.2 UKB annotations
(ii) the UKB LD matrices
and/or
plink bfiles for LD estimation (depending on the LD format of your data) within the resources/ directory.
To ease the running process process, shall be named as follows:
(i) baseline-LF2.2 UKB annotations folder as UKBB_priors
(ii) the UKB LD panel as UKBB_LD
(iii) the plink bfiles for LD estimations as genotype_ref_panel
Links to download these files can be found in the Dependency Wiki page.
All example data were retrieved from
Mullins, N., Forstner, A.J., O’Connell, K.S. et al.
Genome-wide association study of more than 40,000 bipolar disorder cases provides new insights into the underlying biology.
Nat Genet 53, 817–829 (2021).
Downloaded from the PGC website