## Coverage

The function 'coverage.target()' calculates the read coverage for each base that is sequenced (and aligned to the reference) and/or located in a target region. Coverage average and standard deviation are calculated for the target as a whole and for each target region separately. In addition to per-base calculation of read coverage, the numbers of reads falling on each target are given as an alternative measure for target coverage. A read is considered on-target, if it overlaps the target by at least one base.

Average on-target coverage

      > Coverage <- coverage.target(reads, targets, Offset=@OFFSET@)

@AVGCOV@ Statistics table

Coverage per target

      > targetcov <- Coverage$targetCoverages
      > targetcov <- readsPerTarget(reads, targetcov)

@COVTARG@ Full table

Sensitivity

A high sensitivity of the target capture is shown by a large fraction of target bases that are covered by at least 1, 2, 3... reads.

      > covered.k(Coverage$coverageTarget)

@SENSITIVITY@ Sensitivity table

Coverage histogram

Target coverage can be visualized by the coverage histogram. A line is added that shows the cumulative fraction of target bases (right y-axis) with a coverage of at least the corresponding x-axis value. The line represents the results of the previously called function 'covered.k()' for all possible values of k. Additionally, we highlight with dashed lines the target base fraction achieving a coverage of at least 8, in this case.

      > coverage.hist(Coverage$coverageTarget, covthreshold=8)

@COV_HIST@