https://sourceforge.net/p/pb-jelly/discussion/pbhtiks/thread/6ffede16/Recent posts to PBHoney reported coverageenTue, 12 Sep 2017 21:57:26 -0000https://sourceforge.net/p/pb-jelly/discussion/pbhtiks/thread/6ffede16/?limit=25#25e5<div class="markdown_content"><p>Not all reads are mapped in an orientation that allows them to confidently span the region of interest. Additionally, sometimes, alignment of the long-noisy reads using blasr can 'hide' the variant (e.g. supurious matches to bases that have been deleted in order to gain a better alignment score). <br/> Alternate supporting reads those supporting the variant and are fed into the assembly process for refinement.<br/> Reference reads are those that confidently span the region of interest.</p></div>Adam EnglishTue, 12 Sep 2017 21:57:26 -0000https://sourceforge.netf0968bd7b11497915566f7fe02065467518e235fhttps://sourceforge.net/p/pb-jelly/discussion/pbhtiks/thread/6ffede16/?limit=25#4702<div class="markdown_content"><p>Hi Adam,</p> <p>For each call, coverage is reported. However I notice that there tend to be more reads shown in IGV than what is reported as coverage for a region in a VCF.</p> <p>How do you calculate coverage (or which reads do you not include and why)?</p> <p>Best,<br/> Melanie</p></div>Melanie LouThu, 07 Sep 2017 22:39:35 -0000https://sourceforge.net48deb60a6338b7f993cbfb287fdd161cd554a2db