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bam-statistics
95 / 100 · Low risk
Fine to try.
By mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- (GitHub) · other · 36 stars · scanned at commit fde6cd1
Works with any agent that supports SKILL.md skills.
Partially scanned — some files couldn't be read; we'll retry on the next scan
What this skill can do
Runs commands on your computer
The author does not mention this.
Found in 19 places.
Show 16 more
- Skills/Sequence_Analysis/alignment-files/bam-statistics/SKILL.md, line 79
samtools idxstats input.bam - Skills/Sequence_Analysis/alignment-files/bam-statistics/SKILL.md, line 93
samtools idxstats input.bam | awk '{sum += $3} END {print sum}' - Skills/Sequence_Analysis/alignment-files/bam-statistics/SKILL.md, line 107
samtools stats input.bam > stats.txt - Skills/Sequence_Analysis/alignment-files/bam-statistics/SKILL.md, line 112
samtools stats input.bam | grep "^SN" - Skills/Sequence_Analysis/alignment-files/bam-statistics/SKILL.md, line 126
samtools stats input.bam > stats.txt - Skills/Sequence_Analysis/alignment-files/bam-statistics/SKILL.md, line 132
samtools stats input.bam chr1:1000000-2000000 > region_stats.txt - Skills/Sequence_Analysis/alignment-files/bam-statistics/SKILL.md, line 141
samtools depth input.bam > depth.txt - Skills/Sequence_Analysis/alignment-files/bam-statistics/SKILL.md, line 148
samtools depth -r chr1:1000-2000 input.bam - Skills/Sequence_Analysis/alignment-files/bam-statistics/SKILL.md, line 153
samtools depth -a input.bam > depth_with_zeros.txt - Skills/Sequence_Analysis/alignment-files/bam-statistics/SKILL.md, line 158
samtools depth -d 0 input.bam # No cap (default 8000) - Skills/Sequence_Analysis/alignment-files/bam-statistics/SKILL.md, line 163
samtools depth -b regions.bed input.bam - Skills/Sequence_Analysis/alignment-files/bam-statistics/SKILL.md, line 168
samtools depth input.bam | awk '{sum += $3; n++} END {print sum/n}' - Skills/Sequence_Analysis/alignment-files/bam-statistics/SKILL.md, line 176
samtools coverage input.bam - Skills/Sequence_Analysis/alignment-files/bam-statistics/SKILL.md, line 192
samtools coverage -r chr1:1000000-2000000 input.bam - Skills/Sequence_Analysis/alignment-files/bam-statistics/SKILL.md, line 197
samtools coverage -b regions.bed input.bam - Skills/Sequence_Analysis/alignment-files/bam-statistics/SKILL.md, line 202
samtools coverage -m input.bam
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'bam-statistics' ] || [ -L ~/.agents/skills/'bam-statistics' ]; then echo 'A skill folder named bam-statistics already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-' "$d" && git -C "$d" checkout --quiet 'fde6cd1025d8a9300ad783b3d6696fa708a5cdb0' -- 'Skills/Sequence_Analysis/alignment-files/bam-statistics' && mkdir -p ~/.agents/skills && cp -R "$d"/'Skills/Sequence_Analysis/alignment-files/bam-statistics' ~/.agents/skills/'bam-statistics' && rm -rf "$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/'bam-statistics' ~/.claude/skills/'bam-statistics' (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 mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- shows the score of its lowest-scoring skill.

[](https://zalavijaysinh.github.io/skilltrust/repos/mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-/)
Score history
| Date | Version | Score |
|---|
| 2026-11-13 | fde6cd1 | 95 |
| 2026-11-07 | 839c35a | 80 |
Also found in
Identical copies of this skill exist at:
- BioTender-max/awesome-bio-agent-skills/skills/openclaw/bio-alignment-files-bam-statistics