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ukb-gwas-pipeline-nealelab
Pipeline for reproduction of NealeLab 2018 UKB GWAS
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Address GWAS scaling issues
#37
tomwhite
opened
3 years ago
0
Run on preemptible instances
#36
tomwhite
opened
3 years ago
0
Rechunk dosages so there is no chunking in the samples dimension
#35
tomwhite
opened
3 years ago
0
Doc improvements
#34
tomwhite
closed
3 years ago
1
Create VPC
#33
eric-czech
opened
3 years ago
0
Estimate cost of GWAS regression steps
#32
eric-czech
opened
3 years ago
3
Analyze organization of OTG sumstats
#31
eric-czech
opened
3 years ago
0
Debug PHESANT failures after move to filtered samples in inputs
#30
eric-czech
closed
3 years ago
2
Get larger GCP quotas
#29
eric-czech
opened
3 years ago
0
Packer + docker image generation
#28
eric-czech
closed
3 years ago
0
Upgrade to dask 2.30.1+
#27
eric-czech
opened
3 years ago
1
Submit rechunked BGEN zarr archives to UKB returns catalogue
#26
eric-czech
opened
3 years ago
0
Debug snakemake file download failure
#25
eric-czech
closed
3 years ago
9
Create VM image for Dask CP using Packer
#24
eric-czech
closed
3 years ago
0
Upgrade to zarr 2.5.0
#23
eric-czech
closed
3 years ago
1
Figure out how to get dependencies into VM images for Dask CP
#22
eric-czech
closed
3 years ago
4
Getting a GKE cluster working without loadBalancer serviceType
#21
eric-czech
closed
3 years ago
2
Document issues at scale
#20
eric-czech
opened
4 years ago
9
Explore Dask Cloud Provider for deployment
#19
eric-czech
closed
3 years ago
3
Figure out how to identify network bottlenecks
#18
eric-czech
closed
3 years ago
1
Documentation tasks
#17
eric-czech
opened
4 years ago
1
GWAS reproduction tasks
#16
eric-czech
opened
4 years ago
0
Integrate the OT Neale Lab summary stats
#15
eric-czech
opened
4 years ago
1
GWAS script tasks
#14
eric-czech
opened
4 years ago
0
Configure autoscaling for GKE clusters
#13
eric-czech
closed
3 years ago
1
Determine how to set resources for Dask workers on GKE
#12
eric-czech
closed
4 years ago
1
Quantify precision loss in bgen encoding
#11
eric-czech
closed
4 years ago
1
Add support for variant ranges to bgen conversion
#10
eric-czech
closed
3 years ago
1
Store post-QC bgen zarr archives for analysis
#9
eric-czech
closed
3 years ago
6
Estimate costs for complete BGEN conversion
#8
eric-czech
closed
3 years ago
3
Explore using a larger compression block size
#7
eric-czech
closed
4 years ago
1
Decide on an appropriate chunk size for zarr conversions
#6
eric-czech
closed
4 years ago
1
Storage bgen dosage as float16 instead of float32
#5
eric-czech
closed
4 years ago
3
Document expected folder layout
#4
hammer
opened
4 years ago
0
Choose pipeline execution framework
#3
eric-czech
closed
4 years ago
1
How do we evaluate results?
#2
eric-czech
closed
4 years ago
9
What exactly are we trying to reproduce?
#1
eric-czech
opened
4 years ago
0