Versions

Version History

• v0.0.1 (released Sept. 6, 2019)

• v0.0.2 (released Nov. 8, 2019)

  • Fixed file upload issue; up to 3 files may be uploaded at once and file types are auto-detected
  • Increased file size limit to 100 MB
  • Added ability to change the eQTL gene within the plot output page
  • Added interactive table of Simple Sum -log10 P-value results, with ability to download the table in various formats
  • Added t² test for testing whether the given secondary datasets have a significant signal above a Bonferroni adjustment
  • Added ability to upload SNP names in chr_pos_ref_alt_b37 format for cases when the rs ID is not available

• v1.0 alpha (released Dec. 5, 2019)

  • Enabled ability to upload secondary datasets as a merged HTML file in addition to any selected GTEx tissues

• v1.0.1 alpha (released Dec. 18, 2019)

  • Added ability to transpose table and adjust plot figure drawing parameters

• v1.1.0 alpha (released Apr. 1, 2020)

  • Internal change to calculate the Simple Sum using an R script instead of Python.
  • This change enables the use of the app in Windows as the rpy2 package is no longer a requirement

• v1.3.0 alpha (released Jul. 31, 2020)

  • Addition of hg38 coordinate support
  • Added the latest GTEx version 8 (hg38) eQTL analyses for use as secondary datasets for colocalization testing
  • Added GRCh38 re-aligned 1000 Genomes (phase 3) as option for LD matrix
  • Using GENCODE v26 for hg38 gene track
  • Added support for COLOC2 colocalization testing

• v1.4.0 alpha (released Aug. 6, 2020)

  • Added ability to export images as svg vector format
  • Bug fix for the merge_and_convert_to_html_coloc2.py script
  • More sample datasets added that are compatible for COLOC2 runs

• v1.4.1 alpha (Oct. 6, 2020)

  • Bug fix in identifying lead SNP

• v1.4.2 alpha (Oct. 9, 2020)

  • Fixed issue where SS was not being computed due to non-singular matrix error
  • Improved initial plotting time of colocalization plot by filtering out GWAS p-values less than 0.1 by default

• v1.4.3 alpha (Nov. 10, 2020)

  • Fixed issue where the Simple Sum calculation was not being performed in the case where no missing data was present

• v1.4.4 alpha (Nov. 16, 2020)

  • Fixed rsid mapping bug
  • Fixed bug when matching the top SNP with secondary datasets

• v1.4.5 alpha (Feb. 04, 2020)

  • Fixed issue where the SS window did not follow the user-specified lead SNP
  • Added a function to clean up uploaded dataset of common file input reading issues

• v1.4.6 alpha (Feb. 16, 2020)

  • Improved SNP rs ID matching with GTEx rs ID’s
  • Warning text is now displayed if a large number of SNPs do not match variants in GTEx

• v1.4.7 alpha (Feb. 17, 2020)

  • Added output table for parameters used in a particular app run
  • Added output table to help guide and interpret SS colocalization results more easily

• v1.4.8 alpha (Mar. 24, 2020)

  • Fixed SS computation issue when LD matrix has missing values
  • Fixed wrong output for the total number of GTEx datasets in the SS guidance table

  • Note: this version had an issue with uploaded secondary datasets with missing tables where the SS statistics were not assigned to the correct dataset

• v1.4.9 alpha (Apr. 23, 2020)

  • Fixed issue where uploaded secondary datasets with missing tables are properly dealt with

Datasets

• Human reference: hg19 (GRCh37.p13) and hg38 (GRCh38.p7)
• GTEx: versions 7 (hg19) and 8 (hg38)
• GENCODE: version 19 (hg19) (the transcript models were collapsed into a single gene model)
• GENCODE: version 26 (hg38) (the transcript models were collapsed into a single gene model)
• 1000 Genomes (phase 3) aligned to GRCh37 biallelic SNV call set
• 1000 Genomes (phase 3) biallelic SNV call set re-aligned to GRCh38
• dbSNP151 GRCh37.p13
• dbSNP151 GRCh38.p7

Programs

All required programs and versions are specified in the yml file or conda spec file.