SNV Calling

The variant caller runs a series of filters on the set of filtered and realigned reads for SNV calling without affecting indel calls. First, any contiguous trailing sequence of N base calls is trimmed from the ends of reads. Using a mismatch density filter, reads having an unexpectedly high number of disagreements with the reference are masked, as follows:

The variant caller treats each insertion or deletion as a single mismatch.
Base calls with more than 2 mismatches to the reference sequence within 20 bases of the call are ignored.
If the call occurs within the first or last 20 bases of a read, the mismatch limit is applied to a 41-base window at the corresponding end of the read.
The mismatch limit is applied to the entire read when the read length is 41 or shorter.