broadinstitute/gnomad_qc

Issues

• Fix v4 frequency script so all sites are accounted for after splitting dataset in two

  #542 opened a year ago by mike-w-wilson
  1

• Write script to update the freq HT with AN fix

  #541 opened a year ago by mike-w-wilson
  0

• Create script to generate all sites AN file

  #545 opened a year ago by mike-w-wilson
  1

• Add VCF export step to validity check and export VCF code

  #502 opened a year ago by mike-w-wilson
  0

• Update exome release code to account for changes in schema

  #448 opened a year ago by mike-w-wilson
  1

• Write validity checks as part of VCF export pipeline for v4 exomes

  #478 opened a year ago by mike-w-wilson
  0

• Add validity checks to the release HT code

  #474 opened a year ago by mike-w-wilson
  2

• Change 'pop' to 'ga_grp' in release

  #449 opened a year ago by mike-w-wilson
  1

• Generate code for calculating allele frequencies

  #310 opened a year ago by mike-w-wilson
  7

• Add in finalize option to freq script

  #397 opened a year ago by mike-w-wilson
  2

• Determine how to handle partitions with huge numbers of alleles at multiallelic sites for freq

  #412 opened a year ago by mike-w-wilson
  1

• flatten faf and add susbet to meta

  #415 opened a year ago by mike-w-wilson
  0

• Add in non-ukb grpmax and age_hists

  #398 opened a year ago by mike-w-wilson
  1

• Add non-ukb downsamplings

  #400 opened a year ago by mike-w-wilson
  1

• Merge freq_meta_sample_count field

  #399 opened 2 years ago by mike-w-wilson
  0

• Test generate freq code on 2 full partitions

  #370 opened 2 years ago by mike-w-wilson
  1

• Add Tim's adjustments to our code

  #349 opened 2 years ago by mike-w-wilson
  3

• Update adj in frequency script

  #387 opened 2 years ago by mike-w-wilson
  1

• Update freq code to merge all histograms and AB array

  #369 opened 2 years ago by mike-w-wilson
  0

• Update generate_frequency.py script to include optimizations around data reduction

  #360 opened 2 years ago by mike-w-wilson
  1

• Add downsampling split to generate_freq code

  #361 opened 2 years ago by mike-w-wilson
  0

• Update inbreedingcoefficient to work off callstats

  #346 opened 2 years ago by mike-w-wilson
  0

• Add age hist fix to freq code

  #343 opened 2 years ago by mike-w-wilson
  1

• Add qual ab hist fix to code

  #350 opened 2 years ago by mike-w-wilson
  1

• Update frequency code to run on split dataset

  #357 opened 2 years ago by mike-w-wilson
  1

• Annotate and validate globals

  #347 opened 2 years ago by mike-w-wilson
  1

• Adjust sex chromosomes freq calculations

  #348 opened 2 years ago by mike-w-wilson
  1

• Add resource collection

  #345 opened 2 years ago by mike-w-wilson
  0

• Send Tim 2 partition vds for testing

  #344 opened 2 years ago by mike-w-wilson
  1

• Densify chr20 to help estimate full dataset freq cost

  #313 opened 2 years ago by mike-w-wilson
  4

• Remove VEP fields that are universally missing

  #186 opened 2 years ago by gtiao
  2

• Write script to densify and aggregate frequency on chr22 for homalt fix

  #316 opened 2 years ago by mike-w-wilson
  1

• Collect HaplotypeCaller version for all v4 samples

  #312 opened 2 years ago by mike-w-wilson
  3

• HGDP+1KG numbers dont add up

  #315 opened 2 years ago by jerome-f
  1

• question about the trueset dataset

  #308 opened 2 years ago by johjoon
  2

• max_r_het_hom_var

  #281 opened 2 years ago by wym0072003
  2

• combining sparse_matrix tables

  #250 opened 2 years ago by jjfarrell
  1

• Add a note to the gnomad_qc sample_qc hardfilters function that the defaults used are callset specific

  #210 opened 3 years ago by jkgoodrich
  2

• Various small tweaks to improve sanity checks

  #179 opened 3 years ago by gtiao
  4

• PCA loadings for common SNP calculated in gnomad: publicly avaliable?

  #198 opened 3 years ago by WeiCSong
  1

• Have Martin group look over the updated sparse and dense MTs

  #203 opened 3 years ago by jkgoodrich
  2

• Fix simultaneous homalt and het genotyping issue arising due to multi-allelic splitting followed by hotfix for depletion of homozygous alternate genotypes

  #195 opened 3 years ago by gtiao
  5

• Standardize release_ht_path for private ht

  #196 opened 3 years ago by mike-w-wilson
  5

• Score bins Table for v3

  #192 opened 3 years ago by vladsavelyev
  3

• Subpop discussion on Slack or gnomAD meeting

  #202 opened 3 years ago by jkgoodrich
  1

• Make a README for the sample QC and variant QC annotations

  #204 opened 4 years ago by jkgoodrich
  8

• Revise/update README for release-specific code in gnomad_qc repository

  #193 opened 4 years ago by gtiao
  1

• Max SNP # threshold

  #181 opened 4 years ago by vladsavelyev
  4

• Updating v3 subpop notebook to include v3.1 samples

  #194 opened 4 years ago by jkgoodrich
  2

• Applying Random Forest Variant QC

  #199 opened 4 years ago by isstafford
  4