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samtools-bam-processing
80 / 100 · Low risk
Fine to try. Some of what it can do is expected: a coding skill usually runs build and test commands.
By jaechang-hits/SciAgent-Skills (GitHub) · coding · 388 stars · scanned at commit 65d6ceb
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.
Works with any agent that supports SKILL.md skills.
What this skill can do
Runs commands on your computer
The author does not mention this. Expected for a coding skill.
Found in 16 places.
Show 13 more
- skills/genomics-bioinformatics/alignment/samtools-bam-processing/SKILL.md, line 143
samtools fastq -@ 4 -1 R1.fastq.gz -2 R2.fastq.gz -0 unpaired.fastq.gz input.bam - skills/genomics-bioinformatics/alignment/samtools-bam-processing/SKILL.md, line 158
samtools sort -@ 8 -m 2G input.bam -o sorted.bam - skills/genomics-bioinformatics/alignment/samtools-bam-processing/SKILL.md, line 179
samtools flagstat sorted.bam - skills/genomics-bioinformatics/alignment/samtools-bam-processing/SKILL.md, line 201
samtools depth -b target_regions.bed sorted.bam > depth.txt - skills/genomics-bioinformatics/alignment/samtools-bam-processing/SKILL.md, line 221
samtools view -f 2 -F 4 sorted.bam -o proper_pairs.bam - skills/genomics-bioinformatics/alignment/samtools-bam-processing/SKILL.md, line 239
samtools collate -@ 8 -o collated.bam input.bam - skills/genomics-bioinformatics/alignment/samtools-bam-processing/SKILL.md, line 252
samtools markdup -d 2500 sorted.bam marked_novaseq.bam - skills/genomics-bioinformatics/alignment/samtools-bam-processing/SKILL.md, line 267
samtools merge -@ 8 merged.bam lane1.bam lane2.bam lane3.bam - skills/genomics-bioinformatics/alignment/samtools-bam-processing/SKILL.md, line 311
SAMPLE="sample_001" - skills/genomics-bioinformatics/alignment/samtools-bam-processing/SKILL.md, line 336
INPUT="aligned.bam" - skills/genomics-bioinformatics/alignment/samtools-bam-processing/SKILL.md, line 392
for bam in *.sorted.bam; do - skills/genomics-bioinformatics/alignment/samtools-bam-processing/SKILL.md, line 402
samtools view -f 4 -b input.bam -o unmapped.bam - skills/genomics-bioinformatics/alignment/samtools-bam-processing/SKILL.md, line 411
TOTAL=$(samtools flagstat input.bam | grep "mapped (" | head -1 | awk '{print $1}')
Downloads and installs other software
The author does not mention this.
Found in 1 place.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'samtools-bam-processing' ] || [ -L ~/.agents/skills/'samtools-bam-processing' ]; then echo 'A skill folder named samtools-bam-processing already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/jaechang-hits/SciAgent-Skills' "$d" && git -C "$d" checkout --quiet '65d6ceb875e20b751ffb3a6d8ee19516558789e1' -- 'skills/genomics-bioinformatics/alignment/samtools-bam-processing' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/genomics-bioinformatics/alignment/samtools-bam-processing' ~/.agents/skills/'samtools-bam-processing' && rm -rf "$d"; fi
Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'samtools-bam-processing' ~/.claude/skills/'samtools-bam-processing' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.
Badge for your README
The badge for jaechang-hits/SciAgent-Skills shows the score of its lowest-scoring skill.
[](https://zalavijaysinh.github.io/skilltrust/repos/jaechang-hits/SciAgent-Skills/)
Score history
| Date | Version | Score |
|---|
| 2026-11-07 | 65d6ceb | 80 |