bio-consensus-sequences - Generate consensus FASTA sequences from VCF variants
Generates consensus FASTA sequences by applying VCF variants to a reference sequence using bcftools consensus.
Tags
Updated: 2026-09-24Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Apply VCF variants to reference
- Extract sample specific haplotypes
- Encode IUPAC ambiguity codes
- Mask low coverage regions
- Generate coordinate chain files
- Normalize VCF variant records
Inputs
- Reference FASTA file
- VCF variant file
- BED mask file
- BAM alignment file
Outputs
- Consensus FASTA file
- Coordinate chain file
Requirements
- bcftools 1.19+
- samtools 1.19+
- bedtools 2.31+
- minimap2 2.26+
- BioPython 1.83+
- cyvcf2