Scripts from manuscript on analyzing rare diseases in the UK Biobank, "Enhanced Rare Disease Mapping for Phenome-wide Genetic Association in the UK Biobank":
processMapping.sh: Apply consensus mapping to extract rare diseases.
prepareData.sh: Create data table for each rare disease.
Figure1.sh: Plotting scripts for Figure 1.
compareDong.sh: Analysis and plotting to compare comorbidities with previous study by Dong et al.
blairExtract.sh: Extract Mendelian and complex diseases to compare comorbidities with previous study by Blair et al.
blairEnrich.r: Fisher enrichment test and plotting script to compare comorbidities with Blair et al.
annotate.sh: Annotate rare variants from UK Biobank using SnpEff and SnpSift.
grm.sh: Create GRM from UK Biobank Exome sequencing data using SAIGE.
assoc.sh: Association analysis for rare diseases identified through consensus mapping (using SAIGE).
analyzeJAK2.sh: Investigate whether the JAK2 variant is affected by age.