Consensus Tools

consensus_haplotype(
    reference::NucleotideSeq,
    variants::Union{AbstractString,AbstractPath};
    frequency::Float64=0.5,
)

Get the consensus Haplotypefrom variants applied to reference.

Arguments

• reference::NucleotideSeq: Sequence of the reference genome that variants were called from
• variants::Union{AbstractString,AbstractPath}: Path to variant call file that mutations will be applied from

Keywords

• frequency::Float64=0.5: Fraction of total reads that must have supported the alternate position in order to be included as part of the consensus. In other words, only VCF records that have a AF (allele/alternate frequency) higher than this will be considered to contribute to the consensus.

consensus_record(
    reference::Union{AbstractString,AbstractPath},
    variants::Union{AbstractString,AbstractPath};
    frequency::Float64=0.5,
    prefix::Union{AbstractString,Nothing}=nothing,
)

Get the consensus FASTA.Recordfrom variants applied to the first sequence in reference.

Arguments

• reference::Union{AbstractString,AbstractPath}: Path to the reference genome that variants were called from. Only the first sequence will be used.
• variants::Union{AbstractString,AbstractPath}: Path to variant call file that mutations will be applied from

Keywords

• frequency::Float64=0.5: Fraction of total reads that must have supported the alternate position in order to be included as part of the consensus. In other words, only VCF records that have a AF (allele/alternate frequency) higher than this will be considered to contribute to the consensus.
• prefix::Union{AbstractString,Nothing}=nothing: Name to give to the output record. By default, the name of the output record will be the same as the name of the input record with _CONSENSUS appended. If prefix is supplied, then the name of the output record will be $(prefix)_CONSENSUS.