broadinstitute/oncotator

Issues

• the web interface is not available

  #378 opened 4 years ago by DexinYang1998
  0

• Potentially something wrong with the current DB pack?

  #375 opened 5 years ago by JohnMCMa
  9

• Issue with new created datasource

  #376 opened 5 years ago by amomin-pact
  0

• index out range

  #370 opened 7 years ago by bioinfo-dirty-jobs
  4

• COSMIC wrong annotation

  #374 opened 6 years ago by romagnolid
  2

• UniProt 2014_12 not found in uniprot ftp site

  #373 opened 6 years ago by kylec
  0

• Make the source for the web API version available.

  #352 opened 8 years ago by alanhoyle
  6

• error on conotator annotation

  #369 opened 7 years ago by bioinfo-dirty-jobs
  7

• Default Datasource download failed

  #371 opened 7 years ago by fjptwenger
  1

• Malformed VCFs don't generate an error message.

  #354 opened 8 years ago by alanhoyle
  2

• Kitematic/Console installation fails

  #363 opened 8 years ago by leiendeckerlu
  1

• Installation v1.9.2.0 on Ubuntu 14.04.05 failed systematically

  #358 opened 8 years ago by imbeaud
  4

• dbSNP_RS seems to not be annotated with Oncotator 1.9.1 (Broad Internal)

  #357 opened 8 years ago by brendanreardon
  1

• pysam 0.9.0 requirement

  #366 opened 8 years ago by crutching
  0

• Is really only enum34-1.1.2 supported

  #365 opened 8 years ago by mmokrejs
  1

• Installation fails due to python's "SyntaxError: invalid syntax"

  #364 opened 8 years ago by mmokrejs
  1

• Can we distribute the Oncotator through Bioconda?

  #362 opened 8 years ago by holtgrewe
  0

• Oncotator installation

  #361 opened 8 years ago by kamnax
  0

• Docker image broadinstitute/oncotator:1.9.0.0 doesn't have a working ENTRYPOINT or CMD.

  #356 opened 8 years ago by alanhoyle
  3

• Cache filename too long?

  #355 opened 8 years ago by lebolo
  2

• Make the source for the web API version available.

  #353 opened 8 years ago by alanhoyle
  1

• Bio.Data.CodonTable.TranslationError

  #351 opened 8 years ago by ycl6
  2

• initializeDataSource.py dies if the --ds_foldername is an absolute path.

  #350 opened 9 years ago by alanhoyle
  2

• Docker build fails on Step 8 : RUN cd oncotator/ && python setup.py install

  #348 opened 9 years ago by alanhoyle
  22

• Open File Descriptors Issue

  #342 opened 9 years ago by jacmarjorie
  8

• Oncotator VCFInputCreator does not handle SVs gracefully.

  #349 opened 9 years ago by LeeTL1220
  0

• Cannot parse ExAC VCF

  #343 opened 9 years ago by LeeTL1220
  3

• Cannot overwrite annotations when VCF is input

  #345 opened 9 years ago by LeeTL1220
  1

• Fix Travis CI

  #346 opened 9 years ago by LeeTL1220
  2

• Support spanning deletions in VCF input

  #347 opened 9 years ago by LeeTL1220
  0

• Oncotator incorrectly alters reference allele from malformed VCF indels

  #341 opened 9 years ago by crutching
  0

• Oncotator input VCF REF/ALT alleles do not match output alleles

  #340 opened 9 years ago by crutching
  6

• aliased fields in defaults file overwrite populated input fields

  #337 opened 9 years ago by dheiman
  0

• Validation Alleles set as "." or "-"

  #336 opened 9 years ago by Ryan-Singh
  1

• Please set zip_safe to False in setup.py

  #334 opened 9 years ago by holtgrewe
  0

• Webservice HGVS BRCA1 c.3909dupT incorrect

  #333 opened 9 years ago by inodb
  1

• HGVS annotation failing for BRCA mutations

  #316 opened 9 years ago by alexramos
  1

• Oncotator lookup in VCF may not be correct

  #332 opened 9 years ago by LeeTL1220
  0

• MAF To VCF conversion: Need to be able to do the reverse of the M2 aliases

  #320 opened 9 years ago by LeeTL1220
  0

• ONP rendering breaks the OxoG filter (Part II -- field collapsing)

  #326 opened 9 years ago by LeeTL1220
  4

• ONP combining puts "|" separated values in the wrong order

  #329 opened 9 years ago by LeeTL1220
  3

• ONP rendering breaks the OxoG filter (Part I -- re-annotation of TCGA MAF and annotation overwriting)

  #325 opened 9 years ago by LeeTL1220
  5

• VCF does not handle "." in a FORMAT ID field (in the header)

  #328 opened 9 years ago by LeeTL1220
  2

• Oncotator : IndexError exception in the middle of the script

  #321 opened 9 years ago by vigneshravi
  16

• Fix the ``--prepend`` disallowing the AD split

  #323 opened 9 years ago by LeeTL1220
  0

• M2 Phasing information needs to be integrated into infer ONP

  #314 opened 9 years ago by LeeTL1220
  10

• M2 VCF to MAF conversion needs a command line and functionality to support it

  #313 opened 9 years ago by LeeTL1220
  20

• 5'Flank not being rendered

  #315 opened 9 years ago by LeeTL1220
  3

• MAF to VCF conversion needs to combine the read count fields into AD

  #318 opened 9 years ago by LeeTL1220
  0

• Issues still exist in uniprot datasource

  #312 opened 9 years ago by LeeTL1220
  0