broadinstitute/gnomad_local_ancestry

Issues

• Update subsetting script to work with AFR and HGDP + TGP

  #134 opened 7 months ago
  0

• Investigate why 13-72835359-G-A is missing LA data

  #132 opened 3 years ago
  0

• Update blog post migration graphic

  #131 opened 2 years ago
  0

• Enlarge labels on LAI blog post PCA figure

  #130 opened 3 years ago
  0

• Update America to Amerindigenous in code base

  #129 opened 3 years ago
  1

• Update America to Amerindigenous in VCF

  #128 opened 3 years ago
  1

• Validity check imputed sites

  #127 opened 3 years ago
  0

• Convert blog post to markdown

  #126 opened 3 years ago
  1

• Publish blog post

  #125 opened 3 years ago
  0

• Determine message to display for missing LAI data.

  #124 opened 3 years ago
  0

• Draft blog post

  #123 opened 3 years ago
  0

• convert tractor to hail

  #122 opened 3 years ago
  1

• Create gnomAD afr sample subsets for LAI pipeline

  #121 opened 7 months ago
  0

• Run relatedness test on stacey's samples

  #120 opened 3 years ago
  0

• Try mt._localize_entries in VCF adj filtering

  #119 opened 3 years ago
  0

• Present at MPG on 10/14

  #117 opened 3 years ago
  0

• Write blog post for LAI

  #116 opened 3 years ago
  0

• Investigate and respond to Sam Bryant on MacLab archive storage

  #114 opened 3 years ago
  0

• Record and submit LAI presentation

  #113 opened 3 years ago
  0

• Make LAI presentatioon

  #112 opened 3 years ago
  0

• Test gnomix for LAI

  #111 opened 3 years ago
  1

• Rerun pipeline to match gnomAD release counts - HGDP

  #110 opened 3 years ago
  1

• investigate callstat and VCF generation script

  #109 opened 3 years ago
  1

• Investigate Tractor script for counting bug

  #108 opened 3 years ago
  1

• Create README for repo

  #107 opened 3 years ago
  2

• Decide if keeping intermediate files from LAI pipeline.

  #106 opened 3 years ago
  1

• Move LAI VCFs to cheaper regional storage

  #105 opened 3 years ago
  1

• Annotate Alicia's variant spreadsheet with gnomAD AFs

  #104 opened 3 years ago
  0

• LAI VCFs are available for download

  #103 opened 3 years ago
  1

• Investigate Alicia's variants in batch vcfs

  #102 opened 3 years ago
  0

• Look into Tractor's unkinking step for LAI pipeline

  #101 opened 3 years ago
  0

• Fix collapse_ancestry1.py and plot_karyogram1.py

  #100 opened 3 years ago
  0

• Reach out to Steve J to review docker image and bucket set up

  #99 opened 3 years ago
  0

• Frame out ASHG lai presentation

  #98 opened 3 years ago
  0

• Set up meeting with Claire C to discuss presentation narrative

  #97 opened 3 years ago
  2

• Give practice talk at ATGU lab meeting

  #96 opened 3 years ago
  0

• Run accuracy script on simulated data and assess

  #94 opened 3 years ago
  1

• Investigate collapse_ancestry1.py

  #93 opened 3 years ago
  2

• Update Elizabeth's LAI accuracy python script

  #92 opened 3 years ago
  1

• Generate hg38 centromere bed file for plotting painted karyograms

  #91 opened 3 years ago
  0

• Determine official AMR LAI subset

  #90 opened 3 years ago
  1

• Add AF script to batch pipeline

  #89 opened 3 years ago
  0

• Create official LAI 3-way admixed reference panels

  #88 opened 3 years ago
  2

• Create slides for ASHG presentation

  #87 opened 3 years ago
  0

• Determine what to discuss for ASHG presentation

  #86 opened 3 years ago
  0

• Determine what the results file will contain

  #85 opened 3 years ago
  1

• Evaluate simulated data's run through batch lai pipeline

  #84 opened 3 years ago
  4

• Transfer simulated data from Marcos

  #83 opened 3 years ago
  0

• Transfer simulated data from Marcos

  #82 opened 3 years ago
  0

• Phase chr1 test ref panel

  #81 opened 3 years ago
  0