/homegenome

Shiny app for viewing and analyzing 23andMe results

Primary LanguageR

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