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FINNGEN
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autoreporting
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Change low_purity to good_cs, add credset loading from summaries
#161
Lipastomies
closed
3 years ago
1
Separate top report from compare.py
#160
Lipastomies
closed
3 years ago
0
fix online data access
#159
Lipastomies
closed
3 years ago
0
LD partners that are CS variants from other CS should not have any CS-specific data set
#158
Lipastomies
closed
3 years ago
1
Replace low_purity with the good_cs field
#157
Lipastomies
closed
3 years ago
1
credible set grouping wrong LD values
#156
Lipastomies
closed
3 years ago
0
Find out if switch from pytabix to pysam would be beneficial
#155
Lipastomies
closed
3 years ago
1
hand-curated dataset to compare against
#154
Lipastomies
closed
3 years ago
0
Fix gwcatalog api error
#153
Lipastomies
closed
3 years ago
0
Make top report to only consider its own credible set for the credible set column
#152
Lipastomies
closed
3 years ago
0
Create R6 wdl inputs
#151
Lipastomies
closed
3 years ago
0
Add log10 p-value to reports
#150
Lipastomies
closed
3 years ago
0
Gt group report changes
#149
Lipastomies
closed
3 years ago
1
114 PR 3: Add .cred files to WDL
#148
Lipastomies
closed
4 years ago
0
Refactor annotation pipeline
#147
Lipastomies
closed
4 years ago
0
refactor LD API interface
#146
Lipastomies
closed
3 years ago
0
Fixed wrong use of wdl variable.
#145
Fedja
closed
4 years ago
0
Misspecified variable phenoname
#144
sinarueeger
closed
4 years ago
2
add schema for top report in README
#143
Lipastomies
closed
4 years ago
0
Add LD to CS variants in top report
#142
Lipastomies
closed
4 years ago
0
Update readme: WDL documentation
#141
Lipastomies
closed
4 years ago
1
Issue 118, add phenotype information to autoreporting tool
#140
Lipastomies
closed
4 years ago
1
118 PR 3: Add previous release data into WDL pipeline
#139
Lipastomies
closed
4 years ago
0
118 PR 2: change wdl input array to include a dummy file for missing values
#138
Lipastomies
closed
4 years ago
0
118 PR 1: add previous release data to annotations
#137
Lipastomies
closed
4 years ago
0
Explore if open targets genetics could be used
#136
Fedja
opened
4 years ago
1
#114 PR 3: Add credible set information to top report
#135
Lipastomies
closed
4 years ago
0
#114 PR 2: Load information from susie .cred file
#134
Lipastomies
closed
4 years ago
1
#114 PR 1: Change credible set ID format
#133
Lipastomies
closed
4 years ago
0
make PLINK get variant list without duplicates for LD calc
#132
Lipastomies
closed
4 years ago
0
Fixing problems related to scaling with large datasets
#131
Lipastomies
closed
2 years ago
0
Refactor data_access APIs and data structures
#130
Lipastomies
closed
1 year ago
0
loading rows using tabix is slow for large dataframes
#129
Lipastomies
closed
3 years ago
2
Deprecate --finngen-annotation-version
#128
Lipastomies
closed
4 years ago
0
make WDL task fail if the run fails
#127
Lipastomies
closed
4 years ago
0
Deprecate "--finngen-annotation-version"
#126
Lipastomies
closed
4 years ago
1
TODO: Fail wdl task if the autoreporting run inside it fails
#125
Lipastomies
closed
4 years ago
1
remove unused ld_treshold and check_for_ld options from wdl
#124
Lipastomies
closed
4 years ago
0
Remove naming inconsistencies between the main script and wdl parameters
#123
Lipastomies
opened
4 years ago
0
WDL documentation
#122
sinarueeger
opened
4 years ago
2
Issue #96 PR 3: Implement ratelimits for the ensembl API
#121
Lipastomies
closed
4 years ago
0
#96 PR 2: Add check for biallelic variants in ensembl api
#120
Lipastomies
closed
4 years ago
0
Issue #96 PR 1: Move ensembl access out of __get_associations
#119
Lipastomies
closed
4 years ago
0
Add additional information to reports
#118
Fedja
closed
1 year ago
2
Add pairwise LD api for linkage
#117
Lipastomies
opened
4 years ago
2
Refactor grouping functions in gws_fetch
#116
Lipastomies
closed
1 year ago
0
incorrect credible variants
#115
Fedja
closed
4 years ago
2
Add credible set id and bayes factors
#114
Fedja
closed
3 years ago
6
improve documentation
#113
Fedja
opened
4 years ago
0
Fix bugs related to using other data & not having credible sets
#112
Lipastomies
closed
4 years ago
0
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