BWA MEM ValueError: Type names and field names must be valid identifiers: 'P-0052783-N01-WES_IGO_12502_F_1_S12_L001'
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5 months ago

Hi, I am running treeomics tool on VCF file generated by GATK MUTECT2 (and bam file generated by BWA Aligner). I am getting below error. Your help is highly appreciated.

Thanks

Error:
Traceback (most recent call last):
  File "/home/singhh5/miniconda3/envs/treeomics/bin/treeomics", line 33, in <module>
    sys.exit(load_entry_point('treeomics', 'console_scripts', 'treeomics')())
  File "/lila/home/singhh5/software/treeomics/treeomics/__main__.py", line 583, in main
    considered_samples=included_samples, wes_filtering=args.wes_filtering, artifacts=common_vars)
  File "/lila/home/singhh5/software/treeomics/treeomics/patient.py", line 624, in read_vcf_directory
    samples = read_vcf_files(vcf_directory, excluded_samples=excl_samples, considered_samples=considered_samples)
  File "/lila/home/singhh5/software/treeomics/treeomics/utils/vcf_parser.py", line 232, in read_vcf_files
    considered_samples=considered_samples)
  File "/lila/home/singhh5/software/treeomics/treeomics/utils/vcf_parser.py", line 255, in read_vcf_file
    vcf = VCFParser(vcf_file)
  File "/lila/home/singhh5/software/treeomics/treeomics/utils/vcf_parser.py", line 30, in __init__
    self._parse_vcf_file(filename)
  File "/lila/home/singhh5/software/treeomics/treeomics/utils/vcf_parser.py", line 61, in _parse_vcf_file
    named_row = namedtuple('variant', headers)
  File "/home/singhh5/miniconda3/envs/treeomics/lib/python3.7/collections/__init__.py", line 361, in namedtuple
    raise ValueError('Type names and field names must be valid '
ValueError: Type names and field names must be valid identifiers: 'P-0052783-N01-WES_IGO_12502_F_1_S12_L001'
BWA Treeomics • 380 views
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