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Paired End Reads Overlap-Variant Call foreward/reverse reads with high error-rates
Moin from Kiel,
we have an urgent question we currently analyze variants from exon based on amplicons. The short exons are covered by the end of the foreward and reverse read. Unfortunately the error-rate at the end of the reads is quite high. So the region with the high error-rate of both reads covers the exon region. Is reliable call still possible (excluding softclipped reads, reads with low quality,...) due to the high coverange of amplicon-data >20k reads per position. Attached an example from igv (softclipped reads shown as well).