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broadinstitute
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gnomad_local_ancestry
Hail batch pipeline and scripts for local ancestry inference
MIT License
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Create slides for ASHG presentation
#87
mike-w-wilson
closed
2 years ago
0
Determine what to discuss for ASHG presentation
#86
mike-w-wilson
closed
2 years ago
0
Determine what the results file will contain
#85
mike-w-wilson
closed
2 years ago
1
Evaluate simulated data's run through batch lai pipeline
#84
mike-w-wilson
closed
3 years ago
4
Transfer simulated data from Marcos
#83
mike-w-wilson
closed
3 years ago
0
Transfer simulated data from Marcos
#82
mike-w-wilson
closed
3 years ago
0
Phase chr1 test ref panel
#81
mike-w-wilson
closed
3 years ago
0
Subset ref panel to chr1 for simulated data testing
#80
mike-w-wilson
closed
3 years ago
0
Run simulated data through batch LAI pipeline
#79
mike-w-wilson
closed
3 years ago
1
Convert simulated admixed data from hap files to VCF
#78
mike-w-wilson
closed
3 years ago
1
Remove init arg util from batch pipeline
#76
mike-w-wilson
opened
3 years ago
0
Increase batch pipeline memory options for xgmix
#75
mike-w-wilson
closed
3 years ago
1
Mw/add xgmix
#74
mike-w-wilson
closed
3 years ago
1
Determine proper configs for XGMix
#73
mike-w-wilson
closed
3 years ago
1
Investigate XGMix pipeline results
#72
mike-w-wilson
opened
3 years ago
0
Add XGMix to batch pipeline
#71
mike-w-wilson
closed
3 years ago
0
Test AMR chr1 through production pipeline
#68
mike-w-wilson
closed
2 years ago
1
Investigate RFMix2 strand call mimicking
#67
mike-w-wilson
closed
3 years ago
1
Add bgzip command to end of Tractor module
#66
mike-w-wilson
closed
3 years ago
1
Initial commit for MVP LAI batch pipeline
#65
mike-w-wilson
closed
3 years ago
0
LAI in browser
#63
mike-w-wilson
closed
2 years ago
0
Investigate default docker
#62
mike-w-wilson
opened
3 years ago
0
Add plink LD pruning module
#61
mike-w-wilson
opened
3 years ago
0
Add shapeit4 to pipeline
#60
mike-w-wilson
opened
3 years ago
0
Add duohmm module to pipeline
#59
mike-w-wilson
opened
3 years ago
0
Evaluate XGMix as RFMix replacement as local ancestry tool
#58
mike-w-wilson
closed
3 years ago
4
Determine LAI reference panels for admixed AFR individuals within gnomAD (postponed)
#57
mike-w-wilson
opened
3 years ago
1
Determine LAI reference panel for admixed AFR individuals in gnomAD
#56
mike-w-wilson
opened
3 years ago
0
Assess results from gnomAD LAI full production pipeline
#55
mike-w-wilson
closed
2 years ago
0
Build batch pipeline for LAI
#54
mike-w-wilson
closed
2 years ago
0
Determine LAI reference panels for admixed AMR individuals within gnomAD
#53
mike-w-wilson
closed
3 years ago
1
Test if running same reference panel for all admixed Americans (3-way for AMR and AFR gnomAD populations)
#52
mike-w-wilson
opened
3 years ago
2
Download HapMap combined for recombination map
#51
mike-w-wilson
closed
3 years ago
1
Look into XGMix replacing RFMix
#50
mike-w-wilson
closed
3 years ago
1
Overlay rare variants on top of ancestry intervals
#49
mike-w-wilson
opened
3 years ago
0
Create subsets for phasing with and without reference panel
#48
mike-w-wilson
opened
3 years ago
0
Add Tractor to Batch LAI pipeline
#47
mike-w-wilson
closed
3 years ago
0
Add RFMix to Batch LAI pipeline
#46
mike-w-wilson
closed
3 years ago
1
Add Eagle to Batch LAI pipeline
#45
mike-w-wilson
closed
3 years ago
0
Determine file storage for pipeline
#44
mike-w-wilson
closed
3 years ago
1
Create test set for batch pipeline
#43
mike-w-wilson
closed
3 years ago
1
Run PCA on ancestry-specific components for AMR and AFR samples
#42
mike-w-wilson
opened
3 years ago
0
Run PCA on reference panels
#41
mike-w-wilson
closed
3 years ago
0
Learn pattern of admixture in AMR reference panel
#40
mike-w-wilson
opened
3 years ago
0
LAI results are available for download
#39
mike-w-wilson
closed
2 years ago
0
Determine LAI breakdown in browser
#38
mike-w-wilson
closed
2 years ago
2
Overlay rare variants on top of ancestry intervals
#37
mike-w-wilson
closed
3 years ago
0
Investigate larger mixed vs smaller homogenous panel for RFmix
#36
mike-w-wilson
closed
2 years ago
2
Run Tractor on amr pop
#35
mike-w-wilson
closed
2 years ago
0
Estimate initial global ancestry proportion
#34
mike-w-wilson
closed
3 years ago
2
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