bio-pileup-generation skillA
bio-pileup-generation is agent-read markdown (skill) from pku-yuangroup/openai4s: Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies..
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: bcftools 1.19+, 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. # Pileup Generation Generate pileup data for variant calling and position-level analysis. **"Generate pileup from BAM"** -> Produce per-position read summaries showing depth, bases, and qualities. - CLI: `samtools mpileup -f ref.fa input.bam` - Python: `bam.pileup(chrom, start, end)` (pysam) **"Count alleles at a position"** -> Extract per-base read support at a specific genomic coordinate. - Python: iterate `pileup_column.pileups` and count bases (pysam) ## What is Pileup? Pileup shows all reads covering each position in the reference, used for: - Variant calling (with bcftools) - Coverage analysis - Allele frequency calculation - SNP/indel detection …
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How to install
mdr add pku-yuangroup/openai4s/bio-pileup-generation@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-pileup-generation@sha256:0f195a6ab8b8bf77Pin 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_qtqkgzemkycgjudl)
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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