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pysam-genomic-files
75 / 100 · Review before installing
Check before installing. Some of what it can do is expected: a coding skill usually runs build and test commands.
By BioTender-max/awesome-bio-agent-skills (GitHub) · coding · 219 stars · scanned at commit 8cbdd18
Read/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. Region queries, pileup, variant filtering, read groups. Python htslib wrapper exposing samtools/bcftools CLI. Use STAR/BWA for alignment; GATK/DeepVariant for variant calling.
Works with any agent that supports SKILL.md skills.
What this skill can do
Downloads and installs other software
The author does not mention this.
Found in 1 place.
Runs commands on your computer
The author does not mention this. Expected for a coding skill.
Found in 2 places.
Connects to the internet
The author does not mention this.
Found in 19 places.
Show 16 more
- skills/sciagent/pysam-genomic-files/SKILL.md, line 81
for read in inbam.fetch("chr1", 10000, 20000): - skills/sciagent/pysam-genomic-files/SKILL.md, line 126
for record in vcf.fetch("chr1", 10000, 50000): - skills/sciagent/pysam-genomic-files/SKILL.md, line 161
seq = fasta.fetch("chr1", 10000, 10050) - skills/sciagent/pysam-genomic-files/SKILL.md, line 211
WARNING: Uses fetch(until_eof=True), which scans the entire BAM sequentially. - skills/sciagent/pysam-genomic-files/SKILL.md, line 214
for read in bam.fetch("chr1", start, end): ... - skills/sciagent/pysam-genomic-files/SKILL.md, line 220
for read in bam_in.fetch(until_eof=True): - skills/sciagent/pysam-genomic-files/SKILL.md, line 252
for read in bam.fetch(until_eof=True): - skills/sciagent/pysam-genomic-files/SKILL.md, line 310
| pysam Python API | 0-based | exclusive | `fetch("chr1", 999, 2000)` | - skills/sciagent/pysam-genomic-files/SKILL.md, line 311
| samtools region string | 1-based | inclusive | `fetch("chr1:1000-2000")` | - skills/sciagent/pysam-genomic-files/SKILL.md, line 325
Without an index, use `fetch(until_eof=True)` for sequential reading. - skills/sciagent/pysam-genomic-files/SKILL.md, line 410
| `until_eof` | `fetch()` | False | True/False | Read all records sequentially without index | - skills/sciagent/pysam-genomic-files/SKILL.md, line 411
| `multiple_iterators` | `fetch()` | False | True/False | Allow multiple simultaneous iterators (slight overhead) | - skills/sciagent/pysam-genomic-files/SKILL.md, line 420
3. **Use `count()` instead of iterating to count reads**: `bam.count("chr1", 1000, 2000)` is much faster than `sum(1 for _ in bam.fetch(...))`. - skills/sciagent/pysam-genomic-files/SKILL.md, line 438
seq = fasta.fetch(chrom, start, end) - skills/sciagent/pysam-genomic-files/SKILL.md, line 457
for read in bam.fetch(until_eof=True): - skills/sciagent/pysam-genomic-files/SKILL.md, line 484
| Very slow iteration | Iterating all reads without region query | Use `fetch("chr1", start, end)` for targeted queries; use indexed files |
Safer alternatives
Low-risk skills in the same category (coding) that look related. Check that one does what you need.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'pysam-genomic-files' ] || [ -L ~/.agents/skills/'pysam-genomic-files' ]; then echo 'A skill folder named pysam-genomic-files already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/BioTender-max/awesome-bio-agent-skills' "$d" && git -C "$d" checkout --quiet '8cbdd18837aa6296c4e77616a03b323bd69b57b1' -- 'skills/sciagent/pysam-genomic-files' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/sciagent/pysam-genomic-files' ~/.agents/skills/'pysam-genomic-files' && 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/'pysam-genomic-files' ~/.claude/skills/'pysam-genomic-files' (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 BioTender-max/awesome-bio-agent-skills shows the score of its lowest-scoring skill.
[](https://zalavijaysinh.github.io/skilltrust/repos/BioTender-max/awesome-bio-agent-skills/)
Score history
| Date | Version | Score |
|---|
| 2026-11-07 | 8cbdd18 | 75 |