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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
I am trying to filter my HipSTR VCF but am getting the following error:
I'm using the default parameters (below), and get the same error with my VCF and the test VCF in the HipSTR test directory
Any suggestions? Thanks!
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