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FreedomIntelligence/OpenClaw-Medical-SkillsView
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BI
bio-pileup-generation
Maintainer FreedomIntelligence · Last updated April 1, 2026
Generate base-level pileup from BAM for variant calling and coverage.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pileup-generation
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Generate pileup data for variant calling and position-level analysis.
- samtools mpileup -f reference.fa -d 1000 input.bam.
Source Doc
Excerpt From SKILL.md
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
Output Format
Text pileup format (6 columns per sample):
| 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 |
|---|---|
. | Match on forward strand |
, | Match on reverse strand |
ACGT | Mismatch (uppercase = forward) |
acgt | Mismatch (lowercase = reverse) |
^Q | Start of read (Q = MAPQ as ASCII) |
$ | End of read |
+NNN | Insertion of N bases |
-NNN | Deletion of N bases |
* | Deleted base |
> / < | Reference skip (intron) |
Use cases
- Use bio-pileup-generation for genomics and bioinformatics workflows.
- Apply bio-pileup-generation to sequencing, variant, or omics analysis tasks.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- alignment-filtering - Filter BAM before pileup
- reference-operations - Index reference for pileup
- bam-statistics - depth command for coverage
- variant-calling - bcftools call from pileup
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