Clinical-Genomics/genmod

Issues

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

  #67 opened 8 years ago
  2

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

  #66 opened 8 years ago
  2

• VEP Friendly Output

  #65 opened 8 years ago
  2

• Ped File

  #64 opened 9 years ago
  5

• Problem with encodings

  #63 opened 9 years ago
  0

• handle about the GATKHardSNP in VCF header

  #62 opened 9 years ago
  2

• Add support for IMPRECISE variants when querying a ref vcf

  #61 opened 9 years ago
  0

• error with interval-tree

  #60 opened 8 years ago
  5

• GENMOD on bigger VCF file - IO Error

  #58 opened 9 years ago
  3

• Skip families without affected

  #56 opened 9 years ago
  0

• GENMOD output gives pattern of inheritance for familes with no genotype data

  #55 opened 9 years ago
  5

• Genmod writes ExAC_MAX_AF to vcf header when using --thousand_g

  #54 opened 9 years ago
  0

• Catch error and make clean exit

  #53 opened 8 years ago
  0

• Problem with SV alt fields

  #51 opened 9 years ago
  0

• Add COSMIC annotation

  #50 opened 9 years ago
  0

• Build Wiki

  #49 opened 9 years ago
  4

• Problem with compounds when splitted with vt

  #47 opened 9 years ago
  0

• installation issues ?

  #46 opened 9 years ago
  5

• Add support to extract RS number, and MAX_AF from 1000G annotation as new info keys in vcf

  #45 opened 9 years ago
  0

• Add support for MT inheritance models

  #44 opened 9 years ago
  3

• Annotating with CADD Scores

  #43 opened 9 years ago
  12

• Problem with high GQ

  #42 opened 9 years ago
  0

• Reducing AR_comp model noise

  #41 opened 9 years ago
  3

• Modify geneticModels based on reduced penetrance for supplied genes

  #40 opened 9 years ago
  3

• New SO-terms

  #39 opened 9 years ago
  0

• Problems with genmod score

  #38 opened 9 years ago
  0

• Missing compounds

  #37 opened 10 years ago
  11

• 'generate_pairs' is not defined

  #36 opened 10 years ago
  2

• KeyError: u'genmod/configs/rank_model_test_v1.4.ini'

  #35 opened 10 years ago
  5

• Annotating with CADD

  #34 opened 10 years ago
  4

• Annotate with CADD not working

  #33 opened 10 years ago
  1

• Question for X-Linked recessive case analysis

  #31 opened 10 years ago
  4

• Does this work for VCFs with more than one trio?

  #30 opened 10 years ago
  6

• genmod breaking VCF format when adding software tag to header

  #29 opened 10 years ago
  2

• Sort order not respected by genmod

  #28 opened 10 years ago
  3

• Analysing WG quad data- genmod

  #27 opened 10 years ago
  29

• Version 1.5.19 crashing also with test data but with different error

  #26 opened 10 years ago
  2

• Version 1.5.19 crashing

  #25 opened 10 years ago
  2

• Implement genmod analyze

  #24 opened 10 years ago
  1

• Add -strict flag

  #23 opened 10 years ago
  1

• change to relative imports within package

  #22 opened 10 years ago
  0

• AR_comp design

  #21 opened 10 years ago
  16

• Denovo and noCalls

  #20 opened 11 years ago
  9

• Stats from real data indicate that implementation of -phase is a loosening of conditions

  #19 opened 11 years ago
  32

• Erroneous output vcf if input vcf contains variants on multiple chromosomes

  #18 opened 11 years ago
  4

• Runing with -o creates an output file owned by root in pwd

  #17 opened 11 years ago
  2

• Results of running the AR_comp examples with and without -phase

  #16 opened 11 years ago
  3

• Extracting family from VCF file and phasing

  #14 opened 10 years ago
  8

• -phase option does not seem to be in effect

  #13 opened 11 years ago
  7

• IOError: [Errno 13] Permission denied: u'/Lib.....genes.db'

  #11 opened 11 years ago
  2