11/29/2023 0 Comments Annotate exampleIn this example, 829 warnings (Figure 1a) were identified as a result of possible genomic annotation errors or small inconsistencies identified in the reference genome so we have to be careful analyzing those genes/transcripts. The summary file also contains QC information for the gene annotation used as input. Large deviations from the expected values for the organism being sequenced might indicate problems with either the sequencing or variant calling pipelines. In our example, the summary file contains basic quality control statistics calculated from the variant file: for our data, the Ts/Ts ratio is close to 2.0 (Figure 1c) and missense / silent ratio is around 1.0 (Figure 1d), both of which are expected for human data (but these numbers may differ for other species). It can also be created in comma-separated values format (CSV) to be used by downstream processing programs as part of an automated pipeline.
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