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 majiayu000/claude-skill-registry --skill pileup-generation-gptomics-bioskills-1aa7d3ba --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.
# Pileup Generation Generate pileup data for variant calling and position-level analysis. ## 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 ### Basic Pileup ```bash samtools mpileup -f reference.fa input.bam > pileup.txt ``` ### Pileup for Variant Calling (Output BCF) ```bash samtools mpileup -f reference.fa -g input.bam -o output.bcf ``` ### Pileup Specific Region ```bash samtools mpileup -f reference.fa -r chr1:1000000-2000000 input.bam ``` ### Regions from BED ```bash samtools mpileup -f reference.fa -l targets.bed input.bam ``` ### Multiple BAM Files ```bash samtools mpileup -f reference.fa sample1.bam sample2.bam sample3.bam > pileup.txt ``` ## Output Format Text pileup format (6 columns per sample): ``` chr1 1000 A 15 ............... FFFFFFFFFFF chr1 1001 T 12 ............ FFFFFFFFFFFF ``` | Column | Description | |--------|-------------| | 1 | Chromosome | | 2 | Position (1-based) | | 3 | Reference base | | 4 | Read depth | | 5 | Read bases | | 6 | Base qualities | ### Read Bases Encoding | Symbol | Meaning
- What is Pileup?
- samtools mpileup
- Basic Pileup
- Pileup for Variant Calling (Output BCF)
- 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
samtools mpileup -f reference.fa input.bam > pileup.txt samtools mpileup -f reference.fa -g input.bam -o output.bcf 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 Prevent memory issues with high coverage samtools mpileup -f reference.fa -d 1000 input.bam
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 majiayu000/claude-skill-registry --skill pileup-generation-gptomics-bioskills-1aa7d3ba --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 majiayu000/claude-skill-registry, a repository with 534 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.