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alignment-amplicon-clipping

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Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints.

When to use

• Trim PCR primers from aligned reads
• Process SARS-CoV-2 ARTIC panels
• Process hereditary cancer panels
• Process ctDNA hot-spot panels
• Process any amplicon assay
• Soft-clip primer footprints
• Hard-clip primer footprints
• Repair fixmate/MD/NM tags

When not to use

• Processing standard amplicon BAMs with samtools markdup
• Pre-alignment trimming with cutadapt

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