broadinstitute/gnomad_methods

Issues

• filter_vep_transcript_csqs does not work for passing list of CSQ terms

  #707 opened a month ago by mike-w-wilson
  2

• Investigate performance and AC+AF cutoffs for LD Code

  #756 opened a month ago by matren395
  0

• gnomAD toolbox for gnomAD users

  #735 opened 5 months ago by KoalaQin
  0

• Unable to initialize google cluster according to guidelines

  #728 opened 5 months ago by wjwei-handsome
  1

• Meet with Talkowski Group Member / Others about LD Code

  #723 opened 6 months ago by matren395
  1

• Update test_resource_utils.py to eliminate the requester-pays resource testing

  #438 opened 8 months ago by gtiao
  2

• Run code to calculate the average number of mutations per exome and genome in the v4 exome callset

  #704 opened 9 months ago by matren395
  0

• Copy of Run code to calculate the average number of mutations per exome and genome in the v4 exome callset

  #705 opened 9 months ago by matren395
  0

• Document or update split_vds_by_strata to more accurately reflect behavior

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

• Exomes hail table not in public release?

  #670 opened a year ago by allisoncheney
  4

• Variant allele frequency versus population frequency

  #664 opened a year ago by MaryGoAround
  1

• `gks_compute_seqloc_digest` parameter defaults are initializing Hail

  #611 opened a year ago by jkgoodrich
  0

• Investigate doubleton results (missing duplicates)

  #460 opened 3 years ago by ch-kr
  21

• Update tim's annotate_freq_and_high_ab_het function to use passed downsamplings

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

• accessing whole genome vcf for Europeans(Finish and non Finish)

  #562 opened 2 years ago by smhaider
  1

• Unable to securely load ancestry RF model

  #533 opened 2 years ago by poneill
  1

• assign_population_pcs() throws InvalidIndexError when input pop_pca_scores is a Dataframe

  #538 opened 2 years ago by LindoNkambule
  1

• Build function to join multiple frequency arrays into a single freq array

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

• Update annotate_freq to allow specific additional stratafications

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

• Prepare code for sites HT release

  #477 opened 2 years ago by jkgoodrich
  2

• Update annotate_freq to accept multiple groupings for stratification

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

• Is there any command can be used to extract de novo mutations

  #518 opened 2 years ago by xsun1229
  1

• Error of "TypeError: object of type 'NoneType' has no len()" when doing ancestry classification

  #465 opened 2 years ago by Jingning-Zhang
  2

• UnboundLocalError: local variable 'error_rate' referenced before assignment

  #487 opened 2 years ago by PoisonAlien
  3

• Productionize split_context_mt() in the constraint pipeline

  #502 opened 2 years ago by averywpx
  1

• Productionize functions that finalize constraint metrics

  #499 opened 2 years ago by averywpx
  1

• Replace tqdm with rich_progress_bar in file_utils

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

• Test running pre-processing steps of existing constraint pipeline

  #459 opened 3 years ago by ch-kr
  6

• vep_or_lookup_vep failure due to different row types

  #475 opened 3 years ago by mkanai
  8

• Compute QC MT

  #469 opened 3 years ago by jkgoodrich
  0

• KING and pc-relate comparison on v4 test dataset

  #464 opened 3 years ago by ch-kr
  5

• Investigate project name changes between v2 and v4

  #466 opened 3 years ago by ch-kr
  1

• Investigate project name changes between v2 and v4

  #467 opened 3 years ago by ch-kr
  0

• Set up gcloud cluster for v2 constraint testing

  #458 opened 3 years ago by ch-kr
  0

• Compute VDS sample QC

  #455 opened 3 years ago by jkgoodrich
  0

• UnboundLocalError for variable error_rate in assign_population_pcs from sample_qc.ancestry

  #450 opened 3 years ago by LindoNkambule
  1

• Finalize releasable samples for v4

  #442 opened 3 years ago by gtiao
  3

• Public release HT paths need to be updated

  #440 opened 3 years ago by mike-w-wilson
  1

• Set default resource source based on environment

  #433 opened 3 years ago by nawatts
  5

• Sex plodiy cutoffs: lower cutoff for single Y?

  #428 opened 3 years ago by vladsavelyev
  7

• Create new gnomad_methods resources for VDS

  #419 opened 3 years ago by jkgoodrich
  1

• Pin development dependencies

  #424 opened 3 years ago by nawatts
  1

• Decide what metrics to actually use for hard filtering

  #422 opened 3 years ago by jkgoodrich
  1

• Run PCA and ancestry assignment using chosen variants and visualize results

  #418 opened 3 years ago by jkgoodrich
  0

• Resources that do not exist in gnomAD buckets

  #402 opened 4 years ago by nawatts
  2

• Empty `gs://gnomad-public`

  #400 opened 4 years ago by vladsavelyev
  2

• Productionize LoF code

  #393 opened 4 years ago by ch-kr
  2

• Run pylint on gnomad_qc in PR checks

  #396 opened 4 years ago by nawatts
  0

• Re-implement MPC

  #392 opened 4 years ago by ch-kr
  0

• Fix section chi-square values for multiple breaks

  #391 opened 4 years ago by ch-kr
  1