PBHoney reported coverage
Software for Long-Read Sequencing Data from PacBio
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Hi Adam,
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.
How do you calculate coverage (or which reads do you not include and why)?
Best,
Melanie
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).
Alternate supporting reads those supporting the variant and are fed into the assembly process for refinement.
Reference reads are those that confidently span the region of interest.