Why does the Coverage Calculator in the SOPHiA Platform show zero coverage for some genes when other sources indicate there are sufficient reads to detect variants?
In the SOPHiA Platform, the Coverage Calculator shows the worst-case minimum coverage among all of the transcripts. If 0 coverage is observed for some transcripts in a gene, the entire gene is listed with 0 coverage. This can be modified by clicking on the “arrow” next to the gene name, to view all transcripts with well covered exons, as well as transcripts with 0-covered exons within the same gene. For detailed instructions please refer to the Operation Manual Section 4.8.