bio-duplicate-handling skillA
bio-duplicate-handling is agent-read markdown (skill) from pku-yuangroup/openai4s: 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..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
## Version Compatibility Reference examples tested with: picard 3.1+, pysam 0.22+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Duplicate Handling **"Remove PCR duplicates from my BAM file"** -> Mark or remove duplicate reads using the fixmate-sort-markdup pipeline to prevent duplicate bias in variant calling. - CLI: `samtools fixmate`, `samtools markdup` (samtools) - Python: `pysam.fixmate()`, `pysam.markdup()` (pysam) Mark and remove PCR/optical duplicates using samtools. ## Why Remove Duplicates? …
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How to install
mdr add pku-yuangroup/openai4s/bio-duplicate-handling@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-duplicate-handling@sha256:7ef875ece70cd313Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_5fzjmcvdndvmjweo)
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Versions
Audit of the latest version
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_5fzjmcvdndvmjweo GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-duplicate-handling GET https://markdownregistry.com/api/v1/blob/7ef875ece70cd313098b1fb6a4bd977fb1e2b4a4ce76f735c218b5c79a4b35ed
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