Fine-mapping human complex traits with mammalian genome constraint

Code to run polyfun functional fine-mapping with Zoonomia annotations.

Table of contents:

The following code directories are organized by various taskes

code/raw_code:

• ukbb_gwas: download and pre-process the Loh et al. 2018 GWAS
• nonfunct_finemapping: performn non-functional fine-mapping with SuSIE
• make_polyfun_annotations: annotate PolyFun baseline and add Zoonomia annotations
• functional_polyfun_Zoonomia_phyloP_phast_HAR: run PolyFun with only Zoonomia annotations
• functional_polyfun_baseline-LF2.2.UKB: run PolyFun with the BaselineLF2 annotations
• functional_polyfun_Zoonomia_annot_baselineLF2: run PolyFun with the combined annotations

figures/explanatory:

• finemapping_figures: cumulative distribution function plots for Zoonomia Flagship 2 manuscript

figures/exploratory: -comparing_improved_PIP_scores: compare fine-mapped SNPs w/ UNICORNS -functional_polyfun_Zoonomia_phyloP: compare fine-mapped SNPs across annotations

Data:

The following describes the outputs from PolyFun aggregating fine-mapped SNPs across traits data/raw_data/functional_polyfun_Zoonomia_annot_baselineLF2:

• "_top_annot.txt.gz": fine-mapped SNPs along with corresponding annotations
• "_causal_set.txt.gz": fine-mapped SNPs with non-zero PIP