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