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bio-consensus-sequences
Maintainer FreedomIntelligence · Last updated April 1, 2026
Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing haplotypes.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-consensus-sequences
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: bcftools consensus -f reference.fa input.vcf.gz.
- Python: cyvcf2 + Bio.SeqIO for simple SNP-only cases.
- Generate a consensus sequence from my VCF" → Apply called variants to a reference FASTA, producing a sample-specific genome with optional haplotype selection and low-coverage masking. CLI: bcftools consensus -f reference.fa input.vcf.gz Python: cyvcf2 + Bio.SeqIO for simple SNP-only cases.
- 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 when creating sample-specific reference sequences or reconstructing haplotypes.
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
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