Clinical-Genomics/genmod

Issues

• Is `--whole_gene` deprecated?

  #146 opened 7 days ago by fellen31
  2

• "Error: No such option: -f" message when running example

  #127 opened 7 days ago by hrydbeck
  1

• genmod score reorders variants - order not compatible with bgzip & tabix

  #147 opened 11 days ago by fellen31
  0

• genmod score, data_type=string appears to match when the rule is a substring of the string in the VCF

  #87 opened 6 years ago by bjhall
  1

• Compound is missed if one parent is genotyped for each variant

  #99 opened 4 years ago by bartcharbon
  5

• Scoring an empty VCF

  #130 opened 4 months ago by fellen31
  0

• Phased models bugged?

  #126 opened 10 months ago by dnil
  0

• Use poetry

  #143 opened 18 days ago by dnil
  0

• How to interpret two or more inheritance mode given for a variant?

  #145 opened 14 days ago by rfarhad
  0

• "record_rule = max" appears to prioritize based on max(value) rather than max(score)

  #86 opened 6 years ago by bjhall
  2

• String matching in clinvar records..

  #92 opened 17 days ago by dnil
  2

• CSQ field is not parsed properly in genmod score when using --skip_plugin_check

  #85 opened 6 years ago by hassanfa
  2

• Modify rank model for reduced penetrance genes

  #69 opened 8 years ago by henrikstranneheim
  1

• Implement a tier based ranking for somatic mutations

  #95 opened 4 years ago by hassanfa
  3

• ANN standard format

  #96 opened 4 years ago by dridk
  0

• Error occurs if one or more variants in vep annotated VCF lacks VEP annotation when running with --vep

  #105 opened 18 days ago by bartcharbon
  2

• Change or document AR_compound low scoring compound penalty

  #107 opened 2 years ago by dnil
  2

• Silently missing values when using integer format in rank model and encountering a float value

  #128 opened 8 months ago by Jakob37
  2

• Failing update pypi action - add as trusted repo on pypi

  #141 opened 18 days ago by dnil
  4

• Link to documentation broken

  #112 opened 18 days ago by Jakob37
  1

• Genmod compounds control threshold and assigned score

  #137 opened 18 days ago by Jakob37
  0

• Model discrepancy when chrX has chr prefix (GRCh38)

  #132 opened a month ago by fellen31
  0

• Unstable compounds order in output from genmod models

  #133 opened 2 months ago by fellen31
  0

• Malformed INFO lines

  #131 opened 2 months ago by fellen31
  1

• Mixed int-float in RankScore

  #121 opened a year ago by torbjorgen
  0

• TypeError: annotate() got an unexpected keyword argument 'regions'

  #116 opened a year ago by manburst
  2

• python3.10: import error

  #119 opened a year ago by jemten
  1

• container broken for version 3.8

  #115 opened a year ago by jemten
  2

• Tag, build new release

  #113 opened a year ago by torbjorgen
  0

• Food for thought: rank STR expansion variants?

  #84 opened 3 years ago by dnil
  1

• bug in parsing VCF header with filters that use escape character

  #101 opened 4 years ago by hassanfa
  9

• Documentation for "strict" and "phased" seems to be broken

  #100 opened 4 years ago by bartcharbon
  1

• Genmod models '--vep' option throws exception

  #98 opened 4 years ago by bartcharbon
  6

• Incorrect "Compounds" INFO field in case of multiallelic records

  #97 opened 4 years ago by bartcharbon
  2

• no genetic model annotation

  #94 opened 4 years ago by caozongfu
  0

• Some variants without GeneticModels annotation

  #93 opened 5 years ago by geocarvalho
  1

• GenMod error: 'list' object has no attribute 'split'

  #91 opened 5 years ago by fgvieira
  1

• Automatically determine pedigree?

  #89 opened 6 years ago by santiagorevale
  1

• Incompatible CLI with click 7.0

  #90 opened 6 years ago by henrikstranneheim
  0

• No "GeneticModels=" in the output

  #88 opened 6 years ago by jielab
  2

• Compound error in 3.7.1 when single parent

  #82 opened 7 years ago by moonso
  0

• Can not handle when chromosome prefix differs in vcf and resource

  #66 opened 8 years ago by moonso
  2

• Fix SyntaxError due to missing contig length for multisample VCF generated by Freebayes

  #73 opened 8 years ago by nilesh-tawari
  1

• does not work

  #78 opened 8 years ago by brianlamx
  2

• genmod build command does not work

  #74 opened 8 years ago by brianlamx
  0

• VEP Friendly Output

  #65 opened 8 years ago by AndrewSkelton
  2

• vcf_extractor fails to find VEP format for CSQ score model?

  #67 opened 8 years ago by dnil
  2

• Ped File

  #64 opened 8 years ago by AndrewSkelton
  5

• Problem with encodings

  #63 opened 8 years ago by moonso
  0

• handle about the GATKHardSNP in VCF header

  #62 opened 8 years ago by hmkim
  2