pysam-genomic-files SKILL.md skillA
pysam-genomic-files from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/pysam-genomic-files@git:20260929.7a7d60fPins git:20260929.7a7d60f in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 20,762 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Read/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. Region queries, pileup, variant filtering, read groups. Python htslib wrapper exposing samtools/bcftools CLI. Use STAR/BWA for alignment; GATK/DeepVariant for variant calling.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Pysam — Genomic File Toolkit ## Overview Pysam provides a Pythonic interface to htslib for reading, manipulating, and writing genomic data files. It handles SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences with efficient region-based random access. Also exposes samtools and bcftools as callable Python functions. ## When to Use - Reading and querying BAM/CRAM alignment files (region extraction, read filtering) - Analyzing VCF/BCF variant files (genotype access, variant filtering, annotation) - Extracting reference sequences from indexed FASTA files - Calculating per-base coverage and pileup statistics - Building custom bioinformatics pipelines that combine alignment + variant + sequence data - Quality control of NGS data (mapping quality, flag filtering, coverage) - For **alignment from FASTQ** (read mapping), use STAR, BWA, or minimap2 instead - For **variant calling from BAM**, use GATK or DeepVariant instead ## Prerequisites ```bash pip install pysam ``` …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/pysam-genomic-files@sha256:5c30569c42604dc0The line at the top of this page pins the label git:20260929.7a7d60f, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_x2t6thifre7p6el4)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between May 28, 2026 and Sep 29, 2026, about one every 62 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 20,762 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 20,811 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 19,367 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (20762 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_x2t6thifre7p6el4 GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/pysam-genomic-files GET https://markdownregistry.com/api/v1/blob/5c30569c42604dc0da5a49cb9b48354bf5711f1340b5a190746fadf273db1b7b
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.