bio-pileup-generation
Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.
npx skills add BioTender-max/awesome-bio-agent-skills --skill pileup-generation --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: bcftools 1.19+, pysam 0.22+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Pileup Generation Generate pileup data for variant calling and position-level analysis. **"Generate pileup from BAM"** → Produce per-position read summaries showing depth, bases, and qualities. - CLI: `samtools mpileup -f ref.fa input.bam` - Python: `bam.pileup(chrom, start, end)` (pysam) **"Count alleles at a position"** → Extract per-base read support at a specific genomic coordinate. - Python: iterate `pileup_column.pileups` and count bases (pysam) ## What is Pileup? Pileup shows all reads covering each position in the reference, used for: - Variant calling (with bcftools) - Coverage analysis - Allele frequency calculation - SNP/indel detection ## samtools mpileup vs bcftools mpileup (Deprecation) `sa
- Version Compatibility
- What is Pileup?
- samtools mpileup vs bcftools mpileup (Deprecation)
- Basic Pileup
- Pileup Specific Region
- Regions from BED
- Multiple BAM Files
- Output Format
- Read Bases Encoding
- Quality Filtering Options
- Minimum Mapping Quality
- Minimum Base Quality
- Combined Quality Filters
- Maximum Depth (Critical Trap)
samtools mpileup -f reference.fa input.bam > pileup.txt samtools mpileup -f reference.fa -r chr1:1000000-2000000 input.bam samtools mpileup -f reference.fa -l targets.bed input.bam samtools mpileup -f reference.fa sample1.bam sample2.bam sample3.bam > pileup.txt samtools mpileup -f reference.fa -q 20 input.bam samtools mpileup -f reference.fa -Q 20 input.bam samtools mpileup -f reference.fa -q 20 -Q 20 input.bam samtools mpileup default -d 8000 silently truncates targeted / mt-DNA / amplicon / UMI-deduped data bcftools mpileup default -d 250 is far lower; both must be set explicitly when piping samtools mpileup -f reference.fa -d 0 input.bam # no cap
What does the bio-pileup-generation skill do?
Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill pileup-generation --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.