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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 jaechang-hits/SciAgent-Skills (GitHub) · coding · 388 stars · scanned at commit 65d6ceb
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.
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- skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 127
for read in inbam.fetch("chr1", 10000, 20000): - skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 172
for record in vcf.fetch("chr1", 10000, 50000): - skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 207
seq = fasta.fetch("chr1", 10000, 10050) - skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 257
WARNING: Uses fetch(until_eof=True), which scans the entire BAM sequentially. - skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 260
for read in bam.fetch("chr1", start, end): ... - skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 266
for read in bam_in.fetch(until_eof=True): - skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 298
for read in bam.fetch(until_eof=True): - skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 356
| pysam Python API | 0-based | exclusive | `fetch("chr1", 999, 2000)` | - skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 357
| samtools region string | 1-based | inclusive | `fetch("chr1:1000-2000")` | - skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 371
Without an index, use `fetch(until_eof=True)` for sequential reading. - skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 456
| `until_eof` | `fetch()` | False | True/False | Read all records sequentially without index | - skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 457
| `multiple_iterators` | `fetch()` | False | True/False | Allow multiple simultaneous iterators (slight overhead) | - skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 466
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/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 484
seq = fasta.fetch(chrom, start, end) - skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 503
for read in bam.fetch(until_eof=True): - skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 530
| 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=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/jaechang-hits/SciAgent-Skills' "$d" && git -C "$d" checkout --quiet '65d6ceb875e20b751ffb3a6d8ee19516558789e1' -- 'skills/genomics-bioinformatics/alignment/pysam-genomic-files' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/genomics-bioinformatics/alignment/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 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 | 100 |