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.