broadinstitute gnomad_local_ancestry issues

broadinstitute / gnomad_local_ancestry

Hail batch pipeline and scripts for local ancestry inference

MIT License

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Pk split vcf updates

#138 mike-w-wilson closed 4 months ago
0
Add main to subset mt

#137 mike-w-wilson closed 4 months ago
0
add PR suggestions

#136 KoalaQin closed 10 months ago
0
Add HGDP,TGP, and pop option to subset

#135 mike-w-wilson closed 10 months ago
2
Update subsetting script to work with AFR and HGDP + TGP

#134 mike-w-wilson closed 5 months 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 3 years ago
1
Update America to Amerindigenous in VCF

#128 mike-w-wilson closed 3 years ago
1
Validity check imputed sites

#127 mike-w-wilson opened 3 years ago
0
Convert blog post to markdown

#126 mike-w-wilson closed 3 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 3 years ago
0
Draft blog post

#123 mike-w-wilson closed 2 years ago
0
convert tractor to hail

#122 mike-w-wilson opened 3 years ago
1
Create gnomAD afr sample subsets for LAI pipeline

#121 mike-w-wilson closed 5 months ago
0
Run relatedness test on stacey's samples

#120 mike-w-wilson closed 3 years ago
0
Try mt._localize_entries in VCF adj filtering

#119 mike-w-wilson opened 3 years ago
0
Mw/filter to adj

#118 mike-w-wilson closed 3 years ago
0
Present at MPG on 10/14

#117 mike-w-wilson closed 3 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 3 years ago
0
Investigate and respond to Sam Bryant on MacLab archive storage

#114 mike-w-wilson closed 3 years ago
0
Record and submit LAI presentation

#113 mike-w-wilson closed 3 years ago
0
Make LAI presentatioon

#112 mike-w-wilson closed 3 years ago
0
Test gnomix for LAI

#111 mike-w-wilson opened 3 years ago
1
Rerun pipeline to match gnomAD release counts - HGDP

#110 mike-w-wilson closed 3 years ago
1
investigate callstat and VCF generation script

#109 mike-w-wilson closed 3 years ago
1
Investigate Tractor script for counting bug

#108 mike-w-wilson closed 3 years ago
1
Create README for repo

#107 mike-w-wilson opened 3 years ago
2
Decide if keeping intermediate files from LAI pipeline.

#106 mike-w-wilson closed 3 years ago
1
Move LAI VCFs to cheaper regional storage

#105 mike-w-wilson closed 3 years ago
1
Annotate Alicia's variant spreadsheet with gnomAD AFs

#104 mike-w-wilson closed 3 years ago
0
LAI VCFs are available for download

#103 mike-w-wilson closed 3 years ago
1
Investigate Alicia's variants in batch vcfs

#102 mike-w-wilson closed 3 years ago
0
Look into Tractor's unkinking step for LAI pipeline

#101 mike-w-wilson opened 3 years ago
0
Fix collapse_ancestry1.py and plot_karyogram1.py

#100 mike-w-wilson opened 3 years ago
0
Reach out to Steve J to review docker image and bucket set up

#99 mike-w-wilson opened 3 years ago
0
Frame out ASHG lai presentation

#98 mike-w-wilson closed 3 years ago
0
Set up meeting with Claire C to discuss presentation narrative

#97 mike-w-wilson closed 3 years ago
2
Give practice talk at ATGU lab meeting

#96 mike-w-wilson closed 3 years ago
0
Add VCF generation

#95 mike-w-wilson closed 3 years ago
2
Run accuracy script on simulated data and assess

#94 mike-w-wilson closed 3 years ago
1
Investigate collapse_ancestry1.py

#93 mike-w-wilson closed 3 years ago
2
Update Elizabeth's LAI accuracy python script

#92 mike-w-wilson opened 3 years ago
1
Generate hg38 centromere bed file for plotting painted karyograms

#91 mike-w-wilson opened 3 years ago
0
Determine official AMR LAI subset

#90 mike-w-wilson closed 3 years ago
1
Add AF script to batch pipeline

#89 mike-w-wilson closed 3 years ago
0
Create official LAI 3-way admixed reference panels

#88 mike-w-wilson closed 3 years ago
2