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a comma is not a valid field separator ([ \t]+) and is only allowed to be used within a field, so unsure what you're trying to point out.
having the commas can throw off the auto-detection of the actual delimiter so I may have to double check fields 1-3 for whitespace when comma is found.
Columns 9, 11, and 12 can and typically do have commas.
https://bedtools.readthedocs.io/en/latest/content/general-usage.html
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