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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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Add main to subset mt
#137
mike-w-wilson
opened
2 months ago
0
add PR suggestions
#136
KoalaQin
closed
6 months ago
0
Add HGDP,TGP, and pop option to subset
#135
mike-w-wilson
closed
6 months ago
2
Update subsetting script to work with AFR and HGDP + TGP
#134
mike-w-wilson
closed
1 month ago
0
Investigate why 13-72835359-G-A is missing LA data
#132
mike-w-wilson
opened
2 years ago
0
Update blog post migration graphic
#131
mike-w-wilson
closed
2 years ago
0
Enlarge labels on LAI blog post PCA figure
#130
gtiao
closed
2 years ago
0
Update America to Amerindigenous in code base
#129
mike-w-wilson
closed
2 years ago
1
Update America to Amerindigenous in VCF
#128
mike-w-wilson
closed
2 years ago
1
Validity check imputed sites
#127
mike-w-wilson
opened
2 years ago
0
Convert blog post to markdown
#126
mike-w-wilson
closed
2 years ago
1
Publish blog post
#125
mike-w-wilson
closed
2 years ago
0
Determine message to display for missing LAI data.
#124
mike-w-wilson
closed
2 years ago
0
Draft blog post
#123
mike-w-wilson
closed
2 years ago
0
convert tractor to hail
#122
mike-w-wilson
opened
2 years ago
1
Create gnomAD afr sample subsets for LAI pipeline
#121
mike-w-wilson
closed
1 month ago
0
Run relatedness test on stacey's samples
#120
mike-w-wilson
closed
2 years ago
0
Try mt._localize_entries in VCF adj filtering
#119
mike-w-wilson
opened
2 years ago
0
Mw/filter to adj
#118
mike-w-wilson
closed
2 years ago
0
Present at MPG on 10/14
#117
mike-w-wilson
closed
2 years ago
0
Write blog post for LAI
#116
mike-w-wilson
closed
2 years ago
0
Mw/move sub
#115
mike-w-wilson
closed
2 years ago
0
Investigate and respond to Sam Bryant on MacLab archive storage
#114
mike-w-wilson
closed
2 years ago
0
Record and submit LAI presentation
#113
mike-w-wilson
closed
2 years ago
0
Make LAI presentatioon
#112
mike-w-wilson
closed
2 years ago
0
Test gnomix for LAI
#111
mike-w-wilson
opened
2 years ago
1
Rerun pipeline to match gnomAD release counts - HGDP
#110
mike-w-wilson
closed
2 years ago
1
investigate callstat and VCF generation script
#109
mike-w-wilson
closed
2 years ago
1
Investigate Tractor script for counting bug
#108
mike-w-wilson
closed
2 years ago
1
Create README for repo
#107
mike-w-wilson
opened
2 years ago
1
Decide if keeping intermediate files from LAI pipeline.
#106
mike-w-wilson
closed
2 years ago
1
Move LAI VCFs to cheaper regional storage
#105
mike-w-wilson
closed
2 years ago
1
Annotate Alicia's variant spreadsheet with gnomAD AFs
#104
mike-w-wilson
closed
2 years ago
0
LAI VCFs are available for download
#103
mike-w-wilson
closed
2 years ago
1
Investigate Alicia's variants in batch vcfs
#102
mike-w-wilson
closed
2 years ago
0
Look into Tractor's unkinking step for LAI pipeline
#101
mike-w-wilson
opened
2 years ago
0
Fix collapse_ancestry1.py and plot_karyogram1.py
#100
mike-w-wilson
opened
2 years ago
0
Reach out to Steve J to review docker image and bucket set up
#99
mike-w-wilson
opened
2 years ago
0
Frame out ASHG lai presentation
#98
mike-w-wilson
closed
2 years ago
0
Set up meeting with Claire C to discuss presentation narrative
#97
mike-w-wilson
closed
2 years ago
2
Give practice talk at ATGU lab meeting
#96
mike-w-wilson
closed
2 years ago
0
Add VCF generation
#95
mike-w-wilson
closed
2 years ago
2
Run accuracy script on simulated data and assess
#94
mike-w-wilson
closed
2 years ago
1
Investigate collapse_ancestry1.py
#93
mike-w-wilson
closed
2 years ago
2
Update Elizabeth's LAI accuracy python script
#92
mike-w-wilson
opened
2 years ago
1
Generate hg38 centromere bed file for plotting painted karyograms
#91
mike-w-wilson
opened
2 years ago
0
Determine official AMR LAI subset
#90
mike-w-wilson
closed
2 years ago
1
Add AF script to batch pipeline
#89
mike-w-wilson
closed
2 years ago
0
Create official LAI 3-way admixed reference panels
#88
mike-w-wilson
closed
2 years ago
2
Create slides for ASHG presentation
#87
mike-w-wilson
closed
2 years ago
0
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