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Soft-threshold for indels #7

@czakarian

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@czakarian

Hi there!

Really appreciate the work being put into this tool!

I wanted to note that the soft-threshold for the indels doesn't seem to work as described. I will often have indels reported below the soft-threshold, but that don't have the 'low_freq' flag attached. The hard-threshold does work as expected.

Thank you,
Christina

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