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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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Compare trio tracts
#33
mike-w-wilson
opened
3 years ago
0
Plot ancestry karyograms
#32
mike-w-wilson
closed
3 years ago
1
Investigate tract distributions for amr and afr pops
#31
mike-w-wilson
opened
3 years ago
0
Create AFR reference panel for RFMix
#30
mike-w-wilson
opened
3 years ago
0
Create AMR reference panel for RFMix
#29
mike-w-wilson
closed
3 years ago
4
Run RFMix on phased VCFs on amr and afr pops
#28
mike-w-wilson
closed
3 years ago
0
Update subsetted VCFs to variant QC'd variants
#27
mike-w-wilson
closed
3 years ago
0
Phase gnomAD v3.1, 1kG, and HGDP
#26
mike-w-wilson
closed
3 years ago
0
Dummy epic
#25
gtiao
closed
4 years ago
0
Dummy issue
#24
gtiao
closed
4 years ago
0
Pick vignettes for talk: common and rare disease example of variant known to be associated with a specific phenotype, and show how LAI identifies the ancestry of that allele
#23
gtiao
closed
4 years ago
0
Analyze how many variants change frequency once we have local ancestry inference
#22
gtiao
opened
4 years ago
0
Run PCA on the reference panel to get familiar with where ancestry groups lie in PC space
#21
gtiao
opened
4 years ago
0
Overlay rare variants on top of local ancestry intervals (analysis) [Nice to have]
#20
gtiao
opened
4 years ago
0
Create gnomAD LAI release
#19
gtiao
closed
2 years ago
0
Run LAI production pipeline on all gnomAD admixed samples
#18
gtiao
closed
2 years ago
0
Update batch to a production pipeline
#17
gtiao
closed
3 years ago
1
Run script to generate AF spectrums and quality metrics
#16
gtiao
closed
2 years ago
0
Run PCA on ancestry-specific components for AMR samples
#15
gtiao
opened
4 years ago
0
Run full Batch pipeline on each chromosome
#14
gtiao
closed
2 years ago
0
Write scripte to generate allele-frequency spectrums and quality metrics
#13
gtiao
closed
3 years ago
1
Analyze results from chr20 full-pipeline test run
#12
gtiao
closed
2 years ago
1
Run chr20 through complete Batch pipeline (including Tractor)
#11
gtiao
closed
3 years ago
1
Add Tractor to Batch pipeline
#10
gtiao
closed
3 years ago
0
Stress-test Eagle with chr1 for 21k AFR cohort [still needed?]
#9
gtiao
opened
4 years ago
0
Export all per-chromosome VCFs for LAI cohort subset
#8
gtiao
closed
3 years ago
1
Update RFMix Batch pipeline
#7
gtiao
closed
3 years ago
0
Analyze Eagle/RFMix output for AMR chr20 test
#6
gtiao
closed
3 years ago
2
Build Docker image for Batch pipeline
#5
gtiao
closed
3 years ago
1
Test updated Batch pipeline on ~7k AMR samples for chr20
#4
gtiao
closed
3 years ago
0
Export chr20 VCF from gnomAD v3.1 LAI cohort subset
#3
gtiao
closed
3 years ago
0
Subset gnomAD v3.1 to AMR, AFR, HGDP, and 1KG samples from variant QC tables
#2
gtiao
closed
3 years ago
1
Subsets to samples and runs quick variant QC by chromosome
#1
mike-w-wilson
closed
2 years ago
2
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