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When setting up the task (Figure 1), you first need to specify the Genome build and then a Gene/feature annotation file, which defines the genomic regions you are interested in (e.g. exome or genes within a panel). The Gene/feature annotation can be previously associated with Partek Flow via ® Flow® via Library file management or added on the fly.
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| SubtitleText | Setting up Coverage report. The example on the figure shows the use of a custom annotation file, CRCTargets, which defines target regions for a targeted resequencing panel |
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| AnchorName | coverage-dialog |
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Coverage report result page contains project-level overview and starts with a summary table, with one sample per row (Figure 2). The first few columns show the percentage of bases in the genomic features which are covered at the specified level (or higher) (default: 1×, 20×, 100×). Average coverage is defined as the sum of base calls of each base in the genomic features divided by the length of the genomic features. Similarly, Average quality is defined as the sum of average quality of those bases that cover the genomic features, divided by the length of covered genomic features. The last two columns show the number of On-tarted reads (overlapping the genomic features) and Off-target reads (not overlapping the features)....