SNV Calling
The variant caller performs SNV calling on the set of filtered and realigned reads without affecting indel calls. Any contiguous trailing sequence of N base calls is trimmed from the end of the read. Using a mismatch density filter, reads with an unexpectedly high number of disagreements with the reference are masked as follows:
| • | The variant caller identifies each insertion or deletion as a single mismatch. |
| • | Base calls with more than two 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. This limit is applied to a 41-base window at the corresponding end of the read. |
| • | When the read length is 41 or shorter, the mismatch limit is applied to the entire read. |