pseudo_haps {crosshap}

Identify haplotypes from clustered SNPs

Description

pseudo_haps() calls the most common allelic states for each SNP marker group across individuals, before building dummy SNPs for each marker group that mimic the binary vcf format. This is the step which determines the haplotype combinations, and therefore enables several summaries to be returned - as contained in the $Hapfile and preliminary $Indfile and finalised $MGfile, following marker group smoothing. This is an internal function not intended for external use.

Usage

pseudo_haps(preMGfile, bin_vcf, minHap, LD, keep_outliers)

Arguments

preMGfile

SNP clusters from DBscan.

bin_vcf

Binary VCF for region of interest reformatted by run_haplotyping().

minHap

Minimum size (nIndividuals) to keep haplotype combinations

LD

LD matrix input.

keep_outliers

When FALSE, marker group smoothing is performed to remove outliers.

Value

Returns intermediate of haplotype object