Why does the Coverage Calculator in the SOPHiA DDM™ Platform show zero coverage for some genes when other sources indicate there are sufficient reads to detect variants?
In the SOPHiA DDM™ Platform, the Coverage Calculator shows the worst-case minimum coverage among all 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.