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Oncotator bug for VCFs with matching INFO and FILTER tags

danhalligandanhalligan EdinburghMember

I think there is a bug with oncotator when INFO and FILTER fields defined in the header of a VCF file have the same name. For example, with the following VCF (demo.vcf):

##fileformat=VCFv4.1
##FILTER=<ID=PHI,Description="Description of FITLER PHI">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Depth of coverage">
##INFO=<ID=PHI,Number=.,Type=Character,Description="Description of INFO PHI">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
1   10492   .   C   T   1778.2  PHI DP=1934;PHI=C,C,I,I,C,C,C,I,C,I,C

and running:
oncotator -i VCF -o VCF --db-dir dbdir demo.vcf out.vcf hg19

I get the following error:

Verbose mode on
Path:
['/usr/local/bin', '/usr/local/lib/python2.7/site-packages/Oncotator-v1.3.0.0-py2.7.egg', '/usr/local/lib/python2.7/site-packages/leveldb-0.193-py2.7-linux-x86_64.egg', '/usr/local/lib/python2.7/site-packages/natsort-3.5.0-py2.7.egg', '/usr/local/lib/python2.7/site-packages/python_memcached-1.53-py2.7.egg', '/usr/local/lib/python2.7/site-packages/nose-1.3.4-py2.7.egg', '/usr/local/lib/python2.7/site-packages/SQLAlchemy-0.9.7-py2.7-linux-x86_64.egg', '/usr/local/lib/python2.7/site-packages/shove-0.5.6-py2.7.egg', '/usr/local/lib/python2.7/site-packages/Cython-0.21-py2.7-linux-x86_64.egg', '/usr/local/lib/python2.7/site-packages/biopython-1.64-py2.7-linux-x86_64.egg', '/usr/local/lib/python2.7/site-packages/pandas-0.14.1-py2.7-linux-x86_64.egg', '/usr/local/lib/python2.7/site-packages/pysam-0.7.5-py2.7-linux-x86_64.egg', '/usr/local/lib/python2.7/site-packages/distribute-0.6.15-py2.7.egg', '/usr/local/lib/python2.7/site-packages/bcbio_gff-0.5-py2.7.egg', '/usr/local/lib/python2.7/site-packages/stuf-0.9.4-py2.7.egg', '/usr/local/lib/python2.7/site-packages/futures-2.1.6-py2.7.egg', '/usr/local/lib/python2.7/site-packages/pytz-2014.7-py2.7.egg', '/usr/local/lib/python2.7/site-packages/python_dateutil-2.2-py2.7.egg', '/usr/local/lib/python2.7/site-packages/parse-1.4.1-py2.7.egg', '/usr/local/lib/python2.7/site-packages/six-1.8.0-py2.7.egg', '/usr/local/lib/python27.zip', '/usr/local/lib/python2.7', '/usr/local/lib/python2.7/plat-linux2', '/usr/local/lib/python2.7/lib-tk', '/usr/local/lib/python2.7/lib-old', '/usr/local/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/site-packages']

2014-09-25 17:13:44,743 INFO [oncotator.Oncotator:232] Oncotator v1.3.0.0
2014-09-25 17:13:44,743 INFO [oncotator.Oncotator:233] Args: Namespace(cache_url=None, dbDir='dbdir', default_cli=[], default_config=None, genome_build='hg19', infer_genotypes='false', input_file='demo2.vcf', input_format='VCF', log_name='oncotator.log', noMulticore=False, output_file='out.vcf', output_format='VCF', override_cli=[], override_config=None, prepend=False, read_only_cache=False, skip_no_alt=False, tx_mode='CANONICAL', verbose=5)
2014-09-25 17:13:44,744 INFO [oncotator.Oncotator:234] Log file: /home/projects/CGH001_Aridhia/v2/demo-fault/oncotator.log
2014-09-25 17:13:44,744 INFO [oncotator.utils.RunSpecificationFactory:99] no prepend specified when output is not TCGAMAF. Ignoring and proceeding.
2014-09-25 17:13:44,755 WARNING [oncotator.DatasourceFactory:258] %s does not exist, so there will be no datasources.
2014-09-25 17:13:44,755 INFO [oncotator.DatasourceFactory:323] No datasources to initialize
2014-09-25 17:13:44,755 INFO [oncotator.cache.DummyCache:57] No cache specified. All cache attempts will be listed as cache misses.
2014-09-25 17:13:44,756 INFO [oncotator.Annotator:270] Annotating with 0 datasources: Oncotator v1.3.0.0 |
2014-09-25 17:13:44,761 INFO [oncotator.output.VcfOutputRenderer:111] Rendering VCF output file: out.vcf
2014-09-25 17:13:44,767 WARNING [oncotator.Annotator:341] THERE ARE NO DATASOURCES REGISTERED
Traceback (most recent call last):
File "/usr/local/bin/oncotator", line 9, in
load_entry_point('Oncotator==v1.3.0.0', 'console_scripts', 'oncotator')()
File "/usr/local/lib/python2.7/site-packages/Oncotator-v1.3.0.0-py2.7.egg/oncotator/Oncotator.py", line 286, in main
annotator.annotate()
File "/usr/local/lib/python2.7/site-packages/Oncotator-v1.3.0.0-py2.7.egg/oncotator/Annotator.py", line 281, in annotate
filename = self._outputRenderer.renderMutations(mutations, metadata=metadata, comments=comments)
File "/usr/local/lib/python2.7/site-packages/Oncotator-v1.3.0.0-py2.7.egg/oncotator/output/VcfOutputRenderer.py", line 118, in renderMutations
dataManager = OutputDataManager(self.configTable, mutations, comments, metadata, path)
File "/usr/local/lib/python2.7/site-packages/Oncotator-v1.3.0.0-py2.7.egg/oncotator/output/OutputDataManager.py", line 89, in init
self.mutation, self.mutations = self._fetchFirstMutation(muts)
File "/usr/local/lib/python2.7/site-packages/Oncotator-v1.3.0.0-py2.7.egg/oncotator/output/OutputDataManager.py", line 104, in _fetchFirstMutation
for mutation in muts:
File "/usr/local/lib/python2.7/site-packages/Oncotator-v1.3.0.0-py2.7.egg/oncotator/Annotator.py", line 292, in _applyManualAnnotations
for m in mutations:
File "/usr/local/lib/python2.7/site-packages/Oncotator-v1.3.0.0-py2.7.egg/oncotator/Annotator.py", line 300, in _applyDefaultAnnotations
for m in mutations:
File "/usr/local/lib/python2.7/site-packages/Oncotator-v1.3.0.0-py2.7.egg/oncotator/Annotator.py", line 345, in _annotate_mutations_using_datasources
for m in mutations:
File "/usr/local/lib/python2.7/site-packages/Oncotator-v1.3.0.0-py2.7.egg/oncotator/input/VcfInputMutationCreator.py", line 269, in createMutations
yield self._createMutation(record, index, build)
File "/usr/local/lib/python2.7/site-packages/Oncotator-v1.3.0.0-py2.7.egg/oncotator/input/VcfInputMutationCreator.py", line 325, in _createMutation
mut = self._addInfoData2Mutation(mut, record, alt_index)
File "/usr/local/lib/python2.7/site-packages/Oncotator-v1.3.0.0-py2.7.egg/oncotator/input/VcfInputMutationCreator.py", line 204, in _addInfoData2Mutation
number=num)
File "/usr/local/lib/python2.7/site-packages/Oncotator-v1.3.0.0-py2.7.egg/oncotator/MutationData.py", line 124, in createAnnotation
raise DuplicateAnnotationException('Attempting to create an annotation multiple times (' + annotationName + ') with old, new values of (' + str(self.annotations[annotationName].value) + ", " + str(annotationValue) + ")")
oncotator.DuplicateAnnotationException.DuplicateAnnotationException: 'Attempting to create an annotation multiple times (PHI) with old, new values of (FAIL, C,C,I,I,C,C,C,I,C,I,C)'

Tagged:

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Thanks for reporting this -- we've filed an issue, so hopefully that should get fixed in the near future.

  • ImbeaudImbeaud Paris (FranceMember

    Hi,

    Still having the error on vcf.. Using the same command line oncotator -i VCF -o VCF --db-dir dbdir input.vcf out.vcf hg19

    << input.vcf format >>

    fileformat=VCFv4.1

    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Normal Tumor Sample

    1 4241390 . TAG T . PASS IC=2;IHP=2;NT=ref;QSI=64;QSI_NT=64;RC=3;RU=AG;SGT=ref->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50 "30:30:29,37:0,0:1,1:34.6:0.00:0.00" "63:63:24,25:36,45:4,4:64.09:0.35:0.00" CHC1602T

    Having installed the PyVCF provided through your website.
    Any solution for that?

    Kind Regards
    / Sandrine Imbeaud
    [email protected]

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Are you using the latest version of Oncotator?

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