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RareDiseaseAnalysis

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.

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