Off topic:VT tools can`t input reference when attempting to normalize a VCF file
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4.3 years ago
genome21 ▴ 10

When running a normalization function from the Vt tools (http://genome.sph.umich.edu/wiki/Vt) I have:

normalize v0.5

options:     input VCF file                                  DecomposedPilonReducedresult.vcf
         [o] output VCF file                                 VTPilonVCF.vcf
         [w] sorting window size                             10000
         [m] no fail on masked reference inconsistency       false
         [n] no fail on reference inconsistency              false
         [q] quiet                                           false
         [d] debug                                           false
         [r] reference FASTA file                            H37Rv_reference.fasta

[variant_manip.cpp:72 is_not_ref_consistent] failure to extract base from fasta file: AL123456:24697-24715
FAQ: http://genome.sph.umich.edu/wiki/Vt#1._vt_cannot_retrieve_sequences_from_my_reference_sequence_file
Traceback (most recent call last):
  File "/home/mat29/Desktop/FinalReadyPythonSoftwareFeb13-2017/Execute.py", line 128, in normvcf
    execute('bash ./norm.sh')
  File "/home/mat29/.local/lib/python2.7/site-packages/executor/__init__.py", line 166, in execute
    return execute_prepared(ExternalCommand(*command, **options))
  File "/home/mat29/.local/lib/python2.7/site-packages/executor/__init__.py", line 195, in execute_prepared
    command.start()
  File "/home/mat29/.local/lib/python2.7/site-packages/executor/__init__.py", line 1113, in start
    self.wait()
  File "/home/mat29/.local/lib/python2.7/site-packages/executor/__init__.py", line 1156, in wait
    self.check_errors(check=check)
  File "/home/mat29/.local/lib/python2.7/site-packages/executor/__init__.py", line 1274, in check_errors
    raise self.error_type(self)
executor.ExternalCommandFailed: External command failed with exit code 1! (command: bash -c 'bash ./norm.sh')

Does anybody know how to eliminate this errors and what are the reasons?

vcf vttools wgs ngs sequencing • 1.6k views
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