CE
Automation
cellular-senescence-agent
Cellular senescence analysis: marker scoring, SASP profiling, tissue aging assessment.
FreedomIntelligence/OpenClaw-Medical-SkillsView
Automation
CO
consensus-sequences
Maintainer FreedomIntelligence · Last updated April 1, 2026
consensus-sequences.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/consensus-sequences
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Apply variants to reference FASTA using bcftools consensus.
- samtools depth input.bam | awk '$3<10 {print $1"\t"$2-1"\t"$2}' > low_coverage.bed.
Source Doc
Excerpt From SKILL.md
Haplotype Options
| Option | Description |
|---|---|
-H 1 | First haplotype |
-H 2 | Second haplotype |
-H A | Apply all ALT alleles |
-H R | Apply REF alleles where heterozygous |
-I | Apply IUPAC ambiguity codes (separate flag) |
IUPAC Codes for Heterozygous Sites
Heterozygous sites encoded with IUPAC ambiguity codes:
- A/G → R
- C/T → Y
- A/C → M
- G/T → K
- A/T → W
- C/G → S
Mark Low Coverage as N
Using a mask BED file:
Use cases
- Use consensus-sequences in research workflows aligned with this subject area.
- Follow the upstream documentation for the full working procedure.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- variant-calling - Generate VCF for consensus
- filtering-best-practices - Filter variants before consensus
- variant-normalization - Normalize indels first
- alignment-files/reference-operations - Reference manipulation
Related skills
Related skills
DO
Automation
docx
A user may ask you to create, edit, or analy.
FreedomIntelligence/OpenClaw-Medical-SkillsView
FI
Automation
filtering-best-practices
filtering-best-practices.
FreedomIntelligence/OpenClaw-Medical-SkillsView
IM
Automation
image-analysis
image-analysis.
FreedomIntelligence/OpenClaw-Medical-SkillsView