homegenome

Shiny app for viewing and analyzing 23andMe results

Files

• UKBB manifest, incl. wget commands for autodownload
• UKBB heritability estimates
• UKBB phenotype collection notes
• own genome, Sanger-imputed to 22 separate autosomal VCFs
• external allele frequencies (HRC)

Files created by this soft

• dictionary of categories
• login tables (w/ hashed passwords)
• UKBB summary statistics, LD-pruned
• encrypted personal GRS and ClinVar summaries
• various temporary intermediates

Scripts

1. filter-phenofiles.sh to drop boring phenotypes (medications...)
2. download-summaries.sh to wget all the rest, and filter p<1e-5
3. prune-ld.R to clump SNPs based on distance and UKBB association results
4. process-ukbb-cv.R to summarize UKBB and ClinVar reference tables
5. combine-imputed.sh to extract dosages from your Sanger-imputed VCFs
6. combine-imputed2.R to find your GRSs and pathogenic markers
7. app.R - the actual UI and server for Shiny viewer

User process

1. HRC-impute your genotypes in Sanger
2. Have R and packages dplyr, tidyr, sodium
3. Download and run bash combine-imputed.sh
4. Download and run Rscript combine-imputed2.sh
5. Browse to the app, login and enjoy