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pysam
79 / 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 boisenoise/skills-collections (GitHub) · coding · 12 stars · scanned at commit 419c39f
Provides Python/HTSlib workflows for genomic files. Used when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, including pileup, coverage, indexing, and CRAM references.
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 2 places.
Runs commands on your computer
This is disclosed by the author in the skill's SKILL.md or README. Expected for a coding skill.
Found in 2 places.
Connects to the internet
This is disclosed by the author in the skill's SKILL.md or README.
Found in 74 places.
Show 17 more
- skills/kdense-pysam/SKILL.md, line 100
bam.fetch(region="chr1:100-199") # 1-based inclusive - skills/kdense-pysam/SKILL.md, line 122
for read in bam.fetch("chr1", 1_000, 2_000): - skills/kdense-pysam/SKILL.md, line 132
Use `fetch(until_eof=True)` to stream every record in file order, including - skills/kdense-pysam/SKILL.md, line 137
for read in bam.fetch(until_eof=True): - skills/kdense-pysam/SKILL.md, line 143
- `fetch()` returns placed alignment records overlapping a region; even an - skills/kdense-pysam/SKILL.md, line 187
for record in variants.fetch("chr1", 999_999, 2_000_000): - skills/kdense-pysam/SKILL.md, line 216
sequence = fasta.fetch("chr1", 999, 1_099) - skills/kdense-pysam/SKILL.md, line 237
for interval in tbx.fetch("chr1", 1_000, 2_000): - skills/kdense-pysam/SKILL.md, line 260
for read in cram.fetch("chr1", 1_000, 2_000): - skills/kdense-pysam/SKILL.md, line 338
- Treating numeric `VariantFile.fetch()` coordinates as 1-based - skills/kdense-pysam/SKILL.md, line 341
- Assuming `fetch()` includes unplaced unmapped alignments - skills/kdense-pysam/references/alignment_files.md, line 74
for read in bam.fetch("chr1", 1_000, 2_000): - skills/kdense-pysam/references/alignment_files.md, line 82
- BAM/CRAM `fetch()` with no region requires an index and visits placed records - skills/kdense-pysam/references/alignment_files.md, line 85
- SAM `fetch()` without a region is sequential; SAM region access is unsupported - skills/kdense-pysam/references/alignment_files.md, line 92
for read in bam.fetch(until_eof=True): - skills/kdense-pysam/references/alignment_files.md, line 101
`fetch("*")` requests only unplaced unmapped records at the end of a - skills/kdense-pysam/references/alignment_files.md, line 106
`multiple_iterators` belongs to `fetch()`, not the `AlignmentFile`
and 54 more places
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'pysam' ] || [ -L ~/.agents/skills/'pysam' ]; then echo 'A skill folder named pysam already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/boisenoise/skills-collections' "$d" && git -C "$d" checkout --quiet '419c39fde874b8baecbb36a397b967e0190a2ece' -- 'skills/kdense-pysam' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/kdense-pysam' ~/.agents/skills/'pysam' && 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' ~/.claude/skills/'pysam' (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 boisenoise/skills-collections shows the score of its lowest-scoring skill.
[](https://zalavijaysinh.github.io/skilltrust/repos/boisenoise/skills-collections/)
Score history
| Date | Version | Score |
|---|
| 2026-11-12 | 419c39f | 79 |
| 2026-11-08 | 5fe45e5 | 79 |
| 2026-11-06 | b89b2f5 | 79 |
Also found in
Identical copies of this skill exist at:
- LeoYeAI/agent-master-skills/skills/pysam
- stanfish06/skillquarium/skills/pysam