openvax/varcode

Issues

• Add variant and effect classes for gene fusions

  #252 opened 6 months ago by iskandr
  0

• No module named 'pyensembl.biotypes'

  #248 opened 6 months ago by LisaMMilchsack
  0

• Insertion effect from SNV?

  #250 opened a year ago by iskandr
  1

• pyvcf dependency is causing installation failure on setuptools>=58

  #247 opened 3 years ago by susannasiebert
  4

• Update varcode in PyPI

  #249 opened 2 years ago by jonasscheid
  2

• error on nonframeshift deletion

  #246 opened 5 years ago by mpallocc
  1

• Incorrect normalization of "chrM" on GRCh38 to "MT"

  #241 opened 5 years ago by iskandr
  1

• Make liftover between genomes explicit method

  #243 opened 5 years ago by iskandr
  0

• Encountered error during effect sorting due to empty sequence

  #239 opened 5 years ago by iskandr
  0

• Incorrect result (and fix) in effect_ordering.py

  #238 opened 5 years ago by LouieKam
  3

• WT and mutation AA incorrect for variant in codon split across exon boundary

  #236 opened 5 years ago by ijhoskins
  12

• Provide mutation info with StartLosses

  #206 opened 8 years ago by joaoe
  1

• Import of varcode is slow

  #183 opened 6 years ago by joaoe
  3

• Consider alternative effect of ExonicSpliceSite for "top priority"

  #233 opened 6 years ago by iskandr
  0

• Variants before and over the stop codon lose information.

  #202 opened 6 years ago by joaoe
  2

• varcode on Windows throws error: ImportError: No module named 'resource'

  #234 opened 6 years ago by yangli-ai
  4

• README formatting messed up on PyPI

  #177 opened 6 years ago by iskandr
  1

• Add CLI option to automatically run PyEnsembl install()

  #231 opened 6 years ago by iskandr
  1

• Add a `difference` set operation to VariantCollection

  #229 opened 7 years ago by julia326
  0

• Link on PyPI badge broken

  #191 opened 8 years ago by iskandr
  0

• EffectCollection is not sorted by priority by default

  #227 opened 7 years ago by tavinathanson
  0

• Exception when deletion extends beyond exon boundary

  #224 opened 7 years ago by iskandr
  4

• What if the ref allele is a common SNP?

  #215 opened 8 years ago by johannesreiter
  4

• Order of VariantCollection with sort_key=None

  #220 opened 8 years ago by iskandr
  1

• Fix short_description for PrematureStop with empty aa_ref

  #216 opened 8 years ago by joaoe
  1

• Optionally allow duplicated mutations when using load_vcf or load_maf

  #211 opened 8 years ago by tuomastik
  2

• Allow contig to be empty to allow parsing of MAF with faulty mutation(s)

  #210 opened 8 years ago by tuomastik
  5

• Use HGVS format for Silent.short_description

  #217 opened 8 years ago by joaoe
  0

• Allow specification of ensembl release as part of genome on commandline

  #214 opened 8 years ago by iskandr
  0

• Effect prediction throws error (even if raise_on_error=False)

  #213 opened 8 years ago by johannesreiter
  2

• Silent.aa_pos wrong for synonymous SNPs

  #208 opened 8 years ago by joaoe
  1

• Make Varcode correctly infer genome for b37-decoy string

  #207 opened 8 years ago by julia326
  3

• Stoploss confused as insert

  #205 opened 8 years ago by joaoe
  0

• Synonymous Insertion before stop codon annotated as non silent insert

  #201 opened 8 years ago by joaoe
  2

• Varcode noncoding variant in a drop_silent_and_noncoding() list

  #200 opened 8 years ago by ihodes
  2

• Reference incorrectly inferred when "b36" in reference file path

  #181 opened 8 years ago by jburos
  0

• One logger per module

  #196 opened 8 years ago by julia326
  0

• Annotate all transcripts

  #195 opened 8 years ago by joaoe
  4

• SNV results in deletion

  #193 opened 8 years ago by arahuja
  2

• StopLoss pickling is broken

  #188 opened 8 years ago by tavinathanson
  2

• Installation of varcode requires README.md

  #187 opened 8 years ago by iskandr
  1

• Variant effects should contain mutated_sequence

  #179 opened 8 years ago by ihodes
  2

• Synonimous FrameShift over stop codon not annotated as silent

  #168 opened 8 years ago by joaoe
  2

• Insertion of stop codon is annotated as simple Insertion and not PrematureStop

  #169 opened 8 years ago by joaoe
  2

• StopLosses do not translate into 3' UTR

  #170 opened 8 years ago by joaoe
  1

• Mutations before the stop codon confused as StopLosses

  #171 opened 8 years ago by joaoe
  2

• Insertions after the stop codon annotated as plain Insertions

  #172 opened 8 years ago by joaoe
  2

• Wrong aa_ref for insertion of stop codon

  #174 opened 8 years ago by iskandr
  1

• Wrong aa_mutation_end_offset for insertion of stop codon

  #175 opened 8 years ago by iskandr
  3

• Substitution mis-annotated as stop-loss

  #176 opened 8 years ago by iskandr
  1