bcftools-variant-manipulation SKILL.md skillA
bcftools-variant-manipulation 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/bcftools-variant-manipulation@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/variant/bcftools-variant-manipulation/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 19,256 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
CLI for VCF/BCF: filter, merge, annotate, query, normalize, compute stats. Core post-variant-calling: quality filtering, multi-sample merging, rsID annotation, genotype extraction. Samtools companion in HTSlib. Use GATK for complex indel realignment during calling; use VCFtools for population genetics stats.
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
# bcftools — VCF/BCF Variant Manipulation Toolkit ## Overview bcftools is the standard command-line toolkit for processing VCF (Variant Call Format) and BCF (Binary Call Format) files in the HTSlib ecosystem. It covers the complete post-variant-calling workflow: format conversion, quality filtering, variant normalization, multi-sample merging, annotation with external databases, genotype extraction, and QC statistics. bcftools uses streaming by design — most commands read from stdin and write to stdout, making it ideal for memory-efficient pipelines on large cohorts. ## When to Use - Filtering variants by quality (QUAL, DP, AF) after variant calling - Merging VCF files from multiple samples into a joint call set - Adding rsIDs or gene annotations to variant calls - Extracting specific fields (genotypes, allele depths) as tabular output - Normalizing indel representations and splitting multi-allelic records - Calling variants from pileup output (mpileup + call) - Computing per-sample and overall VCF QC statistics - Use `GATK HaplotypeCaller` instead when calling variants with local realignment in human samples …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/bcftools-variant-manipulation@sha256:23e0d796a5668ea9The 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_q7xop2zwcdv4ddq4)
2 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 | 19,256 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 19,305 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 17,379 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 (19256 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_q7xop2zwcdv4ddq4 GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/bcftools-variant-manipulation GET https://markdownregistry.com/api/v1/blob/23e0d796a5668ea99599f6e901b1fdb78d01dce45b8d0a56ef23308894f7ca11
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.