samtools-bam-processing
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.
npx skills add BioTender-max/awesome-bio-agent-skills --skill samtools-bam-processing --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 - Use `deeptools bamCoverage` instead when y
- Overview
- When to Use
- Prerequisites
- Quick Start
- Core API
- Module 1: BAM/SAM I/O and Format Conversion
- Module 2: Sorting and Indexing
- Module 3: Quality Control and Statistics
- Module 4: Read Filtering and FLAG Operations
- Module 5: Duplicate Handling
- Module 6: Multi-file Operations and Region Analysis
- Key Concepts
- SAM FLAG Bits
- CRAM vs BAM vs SAM
Bioconda (recommended) conda install -c bioconda samtools Homebrew (macOS) brew install samtools Verify samtools --version | head -1 Typical post-alignment workflow: sort → index → QC samtools sort -@ 8 -o sorted.bam input.bam samtools index sorted.bam samtools flagstat sorted.bam
What does the samtools-bam-processing skill do?
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.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill samtools-bam-processing --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.