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bio-alignment-files-bam-statistics
Maintainer FreedomIntelligence · Last updated April 1, 2026
Compute alignment statistics: flagstat, idxstats, coverage depth.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-alignment-files-bam-statistics
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Generate alignment statistics using samtools and pysam.
- samtools idxstats input.bam | awk '{sum += $3} END {print sum}.
Source Doc
Excerpt From SKILL.md
Quick Summary Commands
| Command | Output | Speed |
|---|---|---|
flagstat | Read counts by category | Very fast |
idxstats | Per-chromosome counts | Very fast (needs index) |
stats | Comprehensive statistics | Moderate |
depth | Per-position depth | Slow (full scan) |
coverage | Per-region coverage | Fast (needs index) |
samtools flagstat
Fast summary of alignment flags.
Output:
samtools idxstats
Per-chromosome read counts (requires index).
Output format: chrom length mapped unmapped
Use cases
- Use bio-alignment-files-bam-statistics for statistical testing and quantitative analysis.
- Apply bio-alignment-files-bam-statistics to research datasets that require rigorous inference.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- sam-bam-basics - View alignment files
- alignment-indexing - idxstats requires index
- duplicate-handling - Check duplicate rates
- alignment-filtering - Filter before stats
- sequence-io/sequence-statistics - FASTA/FASTQ statistics
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