The Custom/PCR Amplicon workflow evaluates short regions of amplified DNA (amplicons) for variants. The focused sequencing of amplicons enables high-coverage sequencing of particular regions across many samples. The main output files generated by the Custom/PCR Amplicon workflow are BAM files (containing the aligned reads) and VCF files (containing the variant calls).
The Custom/PCR Amplicon workflow supports multiple manifests (containing the probe regions) and consensus sequence reporting for multi-manifest runs.
The Custom/PCR Amplicon workflow can only be used to analyze MiSeq sequencing results
The Custom/PCR Amplicon App Results Page provides a four graphs:
The PCR amplicon Sample Details page provides six panes:
The graphs and variants table display data for the amplicon that is selected in the Amplicon Table.