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bio-ctdna-mutation-detection

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawAnalysisReproductionbio-ctdna-mutation-detection🧬 bioinformatics (gptomics bio-* suite)bioinformatics — clinical databases & variant analysisdetects

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-ctdna-mutation-detection

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • CLI: vardict-java for low-VAF variant calling from cfDNA.
  • 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.

Source Doc

Excerpt From SKILL.md

Input Requirements

RequirementSpecification
Data typeTargeted panel or WES (NOT sWGS)
Depth>= 1000x for low VAF detection
UMIsHighly recommended for < 1% VAF
InputPreprocessed BAM (UMI consensus if available)

VAF Detection Limits

VAF RangeReliabilityNotes
> 1%ReliableStandard callers work
0.5-1%Good with UMIsRequires error suppression
0.1-0.5%ChallengingNeeds deep UMI consensus
< 0.1%UnreliableNear noise floor

Tracking Known Mutations

Goal: Quantify the variant allele fraction of specific known mutations across serial liquid biopsy samples for minimal residual disease monitoring.

Approach: For each target mutation, pileup reads at the variant position, count reference and alternative alleles, and compute VAF with depth statistics.

Use cases

  • Use when identifying tumor mutations from plasma DNA or tracking specific variants.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • cfdna-preprocessing - Preprocess with UMI consensus
  • tumor-fraction-estimation - Estimate overall tumor burden
  • longitudinal-monitoring - Track mutations over time
  • variant-calling/variant-calling - General variant calling concepts

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