bio-ctdna-mutation-detection
Detects somatic mutations in circulating tumor DNA using variant callers optimized for low allele fractions with UMI-based error suppression. Reliably detects mutations at VAF above 0.5 percent using consensus-based approaches. Use when identifying tumor mutations from plasma DNA or tracking specific variants.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-ctdna-mutation-detection --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: Ensembl VEP 111+, SnpEff 5.2+, VarDict 1.8+, pandas 2.2+, pysam 0.22+ 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. # ctDNA Mutation Detection **"Detect mutations in my cfDNA sample"** → Identify somatic variants at low allele fractions (0.1-1%) from cell-free DNA using error-suppressed consensus calling and specialized callers. - CLI: `vardict-java` for low-VAF variant calling from cfDNA Detect somatic mutations in cfDNA at low variant allele fractions. ## Input Requirements | Requirement | Specification | |-------------|---------------| | Data type | Targeted panel or WES (NOT sWGS) | | Depth | >= 1000x for low VAF detection | | UMIs | Highly recommended for < 1% VAF | | Input | Preprocessed BAM (UMI consensus if available) | ## VAF Detection Limits | VAF Range | Reliability | Notes | |------
- Version Compatibility
- Input Requirements
- VAF Detection Limits
- VarDict for High Sensitivity (Ensembl VEP 111+)
- Python Implementation
- UMI-VarCal for Best Specificity (Ensembl VEP 111+)
- Variant Annotation (Ensembl VEP 111+)
- Tracking Known Mutations
- Related Skills
VarDict is highly sensitive for low VAF Use on UMI-consensus BAM for best results vardict-java \ regions.bed | \ teststrandbias.R | \ var2vcf_valid.pl \
What does the bio-ctdna-mutation-detection skill do?
Detects somatic mutations in circulating tumor DNA using variant callers optimized for low allele fractions with UMI-based error suppression. Reliably detects mutations at VAF above 0.5 percent using consensus-based approaches. Use when identifying tumor mutations from plasma DNA or tracking specific variants.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-ctdna-mutation-detection --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 FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 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.