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.
How to install alignment-amplicon-clipping?
gptomics/bioskills/alignment-amplicon-clipping
$npx -y skills add gptomics/bioskills --skill alignment-amplicon-clippingInstalls into the current project.
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Run `npx skills use "https://github.com/gptomics/bioskills" --skill "gptomics/bioskills/alignment-amplicon-clipping"` and follow the generated skill instructions now. Read its complete output, redirecting it to a temporary file first if necessary. Resolve relative paths from the supporting-files directory it provides.
Use the skills in "https://github.com/gptomics/bioskills" that are relevant to the current task. Run `npx skills add "https://github.com/gptomics/bioskills"` and select the relevant skills, then follow their instructions.
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