czbiohub-sf/cerebra

Issues

• count-variants not runnable without specifying cosmicdb

  #110 opened 3 years ago by lincoln-harris
  1

• JoSS Review: Community Guidelines

  #108 opened 4 years ago by betteridiot
  0

• Installation process

  #83 opened 4 years ago by afrubin
  8

• Review comments on CONTRIBUTING.md

  #82 opened 4 years ago by afrubin
  6

• JoSS Review: Quality of writing

  #90 opened 4 years ago by betteridiot
  3

• JoSS Review: Automated Tests

  #107 opened 4 years ago by betteridiot
  0

• JoSS Review: Installation

  #105 opened 4 years ago by betteridiot
  5

• JoSS Review: Functionality

  #106 opened 4 years ago by betteridiot
  3

• hgvs throwing stdout

  #99 opened 4 years ago by lincoln-harris
  0

• JoSS Review: Clarify README.md

  #89 opened 4 years ago by betteridiot
  3

• zlib error

  #101 opened 4 years ago by lincoln-harris
  2

• vcfpy exception

  #103 opened 4 years ago by lincoln-harris
  2

• Supporting different types of annotation GTFs

  #36 opened 4 years ago by rvanheusden
  2

• would like to make cerebra modules importable

  #97 opened 4 years ago by lincoln-harris
  0

• improve testing speed

  #85 opened 4 years ago by lincoln-harris
  3

• setup docker container

  #51 opened 4 years ago by lincoln-harris
  2

• trouble adding to bioconda

  #92 opened 4 years ago by lincoln-harris
  0

• pysam build fails on python3.8

  #86 opened 4 years ago by lincoln-harris
  5

• Versioning question

  #78 opened 4 years ago by afrubin
  0

• Python 3.8 support

  #80 opened 4 years ago by afrubin
  0

• Requirements and CI

  #79 opened 4 years ago by afrubin
  0

• Universal wheel

  #81 opened 4 years ago by afrubin
  0

• output json instead of csv

  #48 opened 4 years ago by lincoln-harris
  2

• make germline-filter module more robust

  #67 opened 4 years ago by lincoln-harris
  2

• consider changing mutations -> variants in module names

  #71 opened 4 years ago by lincoln-harris
  1

• add prebuilt index for genome.fa

  #70 opened 4 years ago by lincoln-harris
  2

• germline-filter run instructions

  #53 opened 4 years ago by not-rs
  5

• perhaps give non-tumor cells better names for germline filtering

  #22 opened 4 years ago by rvanheusden
  0

• add comprehensive test for germline_filter

  #66 opened 4 years ago by lincoln-harris
  1

• filtered_cosmic_db in count_mutations.py limiting to lung

  #65 opened 4 years ago by lincoln-harris
  1

• filtered_cosmic_db in find_aa_mutations limiting to lung

  #63 opened 4 years ago by lincoln-harris
  0

• wierd Bioseq install error -- package not found

  #59 opened 4 years ago by lincoln-harris
  1

• JOSS guidelines

  #54 opened 4 years ago by lincoln-harris
  0

• multiprocessing race condition

  #47 opened 5 years ago by lincoln-harris
  10

• clarification on AD field of vcf files

  #52 opened 5 years ago by lincoln-harris
  2

• not picking up intronic variants

  #18 opened 5 years ago by lincoln-harris
  0

• look into potential changes in mutation_counts functionality due to GenomePosition.from_vcf_record change

  #28 opened 5 years ago by rvanheusden
  1

• vcf '20' field is sometimes malformed

  #25 opened 5 years ago by lincoln-harris
  1

• need to integrate gvcf search into coverage module

  #27 opened 5 years ago by lincoln-harris
  0

• find-aa-mutations not working, post-merge with Rohan's branch

  #41 opened 5 years ago by lincoln-harris
  2

• improve germline filtering: handle multiple ALTs better

  #24 opened 5 years ago by rvanheusden
  1

• during vcf reconstruction (germline filter) step, we're literally appending the same vcf header to all our files

  #16 opened 5 years ago by lincoln-harris
  2

• germline_filter.py requires 'ID' field to match...this probably makes things too strict

  #14 opened 5 years ago by lincoln-harris
  2

• when we reconstruct vcfs during the germline filter step, we excluded the 2 last columns

  #15 opened 5 years ago by lincoln-harris
  3

• GenomePosition.from_str shouldn't assume 1-index

  #26 opened 5 years ago by rvanheusden
  0

• need to integrate coverage module

  #19 opened 5 years ago by lincoln-harris
  2

• refactor check_coverage module to work on gene-level, rather than with a user-defined set of ROIs

  #23 opened 5 years ago by lincoln-harris
  1

• add dbSNP filter, probably in germline_filter.py module

  #21 opened 5 years ago by lincoln-harris
  2

• vcf and cosmic appear to disagree about the strandedness for certain genes?

  #20 opened 5 years ago by lincoln-harris
  1

• how does utils.get_best_overlap deal with genome positions that have multiple hits

  #17 opened 5 years ago by lincoln-harris
  1