samtools-bam-processing SKILL.md skillA
samtools-bam-processing 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/samtools-bam-processing@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/samtools-bam-processing/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 16,395 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat, stats, depth, markdup, merge. Required between alignment and variant/peak calling. Use pysam for Python-native BAM access; deeptools for normalized coverage tracks.
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
# samtools — SAM/BAM/CRAM Alignment Toolkit ## Overview samtools is the standard command-line toolkit for processing sequence alignment files in SAM, BAM, and CRAM formats. It handles the complete alignment file lifecycle: format conversion, coordinate sorting, index creation, quality control statistics, read filtering, duplicate marking, and multi-file merging. samtools is a near-universal component of NGS pipelines between alignment (STAR, BWA) and downstream analysis (variant calling, peak calling, coverage). ## When to Use - Sorting BAM files by coordinate after alignment (required before indexing) - Indexing sorted BAM files for random access and region queries - Converting between SAM, BAM, and CRAM formats to save storage - Generating alignment QC metrics: mapping rates, insert sizes, per-chromosome stats - Filtering reads by mapping quality, FLAG bits, or genomic regions - Marking or removing PCR duplicates before variant calling - Merging multiple BAM files from different lanes or samples - Calculating per-base depth or coverage breadth for target regions - Use `pysam` instead for Python-native BAM manipulation in custom scripts …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/samtools-bam-processing@sha256:7bab664765288028The 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_bahiohevjpdbiogd)
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 | 16,395 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 16,444 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 14,440 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 (16395 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_bahiohevjpdbiogd GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/samtools-bam-processing GET https://markdownregistry.com/api/v1/blob/7bab664765288028a3e67f88ea43bc1e0901744fa5b469349ec040092eb6ff95
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