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EBISPOT
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gwas-sumstats-harmoniser
GWAS Summary Statistics Data Harmonisation
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Failed site handling
#56
jdhayhurst
closed
1 year ago
0
Failed site handling
#55
jdhayhurst
closed
1 year ago
0
Docker img
#54
jdhayhurst
closed
1 year ago
1
0 beta values are converted to NA in hm_beta
#53
jdhayhurst
closed
1 year ago
0
liftover is performed using 1-based coordinates against a 0-based chain file
#52
jonaszierer
opened
1 year ago
0
Query over GCST90010715 harmonisation
#51
jinghuazhao
closed
1 year ago
1
harmonised file conforms to new standard format
#50
jdhayhurst
closed
1 year ago
4
pipeline reads build from metadata
#49
jdhayhurst
closed
1 year ago
3
harmonisation pipeline generates sumstats metadata in correct format
#48
jdhayhurst
closed
1 year ago
0
adding coordinate conversion method
#47
jdhayhurst
closed
2 years ago
0
config parser, removing config from map to build
#46
jdhayhurst
closed
2 years ago
0
dynamically manage harmonisation args
#45
jdhayhurst
closed
2 years ago
0
publish harmonisation pipeline resources on FTP
#44
jdhayhurst
closed
2 years ago
1
Annotate variants with "mapping method"
#43
jdhayhurst
closed
1 year ago
1
Make input for harmonisation more configurable/flexible
#42
jdhayhurst
closed
1 year ago
2
refactor configs
#41
jdhayhurst
closed
1 year ago
1
Nextflow
#40
jdhayhurst
closed
1 year ago
5
update dev
#39
jdhayhurst
closed
2 years ago
0
Review latest harmonisation developments
#38
jdhayhurst
closed
1 year ago
1
Develop a solution for monitoring the harmonisation pipeline
#37
jdhayhurst
opened
2 years ago
1
Write the file stager/filter for the harmonisation pipeline
#36
jdhayhurst
closed
2 years ago
3
Write a launcher to initiate the Nextflow driver
#35
jdhayhurst
closed
1 year ago
1
Rewrite and modify the snakemake pipeline with Nextflow
#34
jdhayhurst
closed
7 months ago
3
Bump numpy from 1.18.4 to 1.22.0
#33
dependabot[bot]
closed
5 months ago
1
Bump numpy from 1.18.4 to 1.21.0
#32
dependabot[bot]
closed
2 years ago
1
Merge pull request #26 from EBISPOT/dev
#31
jdhayhurst
closed
2 years ago
0
Add step to normalise variants
#30
jdhayhurst
opened
2 years ago
1
Develop plan for transferring harmonised files from GDP to GWAS Catalog
#29
aoifemcm
opened
2 years ago
1
Improve tracking and versioning of harmonisation pipeline
#28
aoifemcm
opened
2 years ago
1
Update of harmonisation pipeline
#27
jiyue1214
closed
2 years ago
0
Dev
#26
jdhayhurst
closed
2 years ago
0
Merge in OTAR harmoniser
#25
jdhayhurst
closed
2 years ago
1
After harmonisation, if file could not be harmonised, produce a short report to explain why
#24
jdhayhurst
closed
1 year ago
13
reorder dockerfile, adding tabix
#23
jdhayhurst
closed
2 years ago
0
fix path for submodule
#22
jdhayhurst
closed
2 years ago
0
adding submodule, updating gitlab-ci
#21
jdhayhurst
closed
2 years ago
0
Dockerise
#20
jdhayhurst
closed
2 years ago
0
Improve efficiency of pipeline
#19
jdhayhurst
closed
2 years ago
6
tabix harmonised sumstats files
#18
jdhayhurst
closed
1 year ago
1
investigate why pipeline gets locked on occasions
#17
jdhayhurst
closed
1 year ago
1
Bump urllib3 from 1.25.9 to 1.26.5
#16
dependabot[bot]
closed
5 months ago
1
Bump pyyaml from 5.3.1 to 5.4
#15
dependabot[bot]
closed
5 months ago
1
Need to QC non-rsID type variant IDs
#14
jdhayhurst
opened
3 years ago
0
investigate files that are failing to harmonise
#13
jdhayhurst
closed
3 years ago
0
non mandatory columns for the harmonisation, should not be mandatory
#12
jdhayhurst
closed
2 years ago
1
Check that these codes are represented in the harmonised data: 14, 15, 16, and 9
#11
jdhayhurst
closed
3 years ago
2
duplicated rows in output
#10
jdhayhurst
closed
3 years ago
2
harmonisation failures due to numerical values: "."
#9
jdhayhurst
closed
3 years ago
0
fix for unmappable rsids
#8
jdhayhurst
closed
4 years ago
0
harmonisation doesn't complete for certain datasets
#7
jdhayhurst
closed
4 years ago
0
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