Future Directions

LocusFocus is open source and continuously undergoing development and improvements.

Below is a list of improvements and features currently under development:

  • Enable uploading of compressed files (then convert to bgzip/tabix)
  • Implement a queue system to enable job submission and later retrieval
  • Enable ability to upload a config file to replicate results
  • Implement SMR colocalization method
  • Enable immediate deletion of the session data
  • Enable option to match variant names by just chrom:pos information (currently should only be either all rsid’s or all variant_id format)
  • Generate updated 1KG Phase 3 binary PLINK files for hg19 LD calculations (currently only have 2012 1KG file)
  • Enable user to set the window sizes for eQTL lines; and make calculation clearer
  • Make a table of GWAS and eQTL merged results
  • Plot of beta correlations
  • Make P-P plot

A list of known bugs currently being addressed:

  • chrX plots do not show correctly
  • SS coordinate input field checking not working - should also check if it’s a subregion of full coordinate/locus region
  • Remove related individuals prior to calculating LD from the 1000 Genomes
  • Include option for NFE LD (Non-Finnish European subset) for hg19 1000 Genomes
  • File too large error handler not working
  • Fix COLOC2 chromosome X issue
  • Add requirement for having REF and ALT columns for secondary datasets for better SNP matching