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issue with filtering VCF #2

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hannah-happ opened this issue Jan 11, 2024 · 0 comments
Open

issue with filtering VCF #2

hannah-happ opened this issue Jan 11, 2024 · 0 comments

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@hannah-happ
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hannah-happ commented Jan 11, 2024

I am trying to filter my HipSTR VCF but am getting the following error:

Traceback (most recent call last):
 File "/scratch/ucgd/lustre-work/quinlan/u6055472/storage/tools/HipSTR/scripts/filter_vcf.py", line 233, in <module>
  main()
 File "/scratch/ucgd/lustre-work/quinlan/u6055472/storage/tools/HipSTR/scripts/filter_vcf.py", line 94, in main
  vcf_writer  = vcf.Writer(sys.stdout, vcf_reader)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 File "/scratch/ucgd/lustre-work/quinlan/u6055472/storage/tools/miniconda3/lib/python3.11/site-packages/vcf/parser.py", line 642, in __init__
  self.writer = csv.writer(stream, delimiter="\t",
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: "quotechar" must be a 1-character string

I'm using the default parameters (below), and get the same error with my VCF and the test VCF in the HipSTR test directory

python ${scripts}/filter_vcf.py --vcf ${VCF_DIR}/str_calls.vcf --min-call-qual 0.9 --max-call-flank-indel 0.15 --max-call-stutter 0.15 --min-call-allele-bias -2 --min-call-strand-bias -2

Any suggestions? Thanks!

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