This is a general question about the inner-working of interval filtration (i.e. --intervals, -L parameters with a supplied "intervals"-containing file). Since this functionality is provided for a good number of tools in the GATK toolkit, I was trying to find documentation/explanations of how filtration actually proceeds.
I'm wondering, in particular, if it checks every read (independently of mate information) and filters the read if it doesn't overlap any provided intervals (thus leaving behind singleton reads if one partner in a read pair doesn't overlap with an RoI). What constitutes as overlap -- a single position between a read and an interval? Also, do secondary and/or supplementary reads get any special treatment, or are they treated the same way as primary alignments?
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