Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.
How to install duplicate-handling?
gptomics/bioskills/duplicate-handling
$npx -y skills add gptomics/bioskills --skill duplicate-handlingInstalls into the current project.
›Prefer a prompt? Paste this to your agent
Run `npx skills use "https://github.com/gptomics/bioskills" --skill "gptomics/bioskills/duplicate-handling"` 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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