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Amplicon analysis

Amplicon are by nature duplicated. By default most reads will therefore be ignored by freebayes or filter at the sambamba step.

In the config section, you can undo the mark_duplicate step.

Another common issue with amplicon is that you may have poor quality at the end of your read that will be trimmed/clipped. This can be checked in the coverage where you may see drop of coverage. You can twick the bwa option. For instance, you may ad -B0 to prevent mismatches to be penalised.

With amplicon, you may expect the coverage to be very large. The samtools depth command used in the pipeline has a limitation of 20,000X. If you see a coverage at 20,000 X be aware that it means you may have even more coverage.