Phasing trios

Description

compute compound gentoype for trios from sequencing data

Usage

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FamilyPhase(parent.genotype, child.genotype)
FamilyPhaseII(parent.genotype, child.genotype)
FamilyPhaseIII(parent.genotype, child.genotype)
PairPhase(paternal.genotype, child.genotype)

Arguments

parent.genotype

matrix, parents genotype

child.genotype

vector, child gentoype

paternal.genotype

vector, genotype of one parent

Details

PairPhase: sharing analysis between one parent and child FamilyPhase: compute cpmpound genotype for trios when parents do not share any variants FamilyPhaseII: compute cpmpound genotype for trios. when parents share heterozygous variants, remove shared variants and perform test FamilyPhaseIII: compute cpmpound genotype for trios. when parents share heterozygous variants, set family as missing data,used in current analysis

Value

3 elements vector: paternal compound genotype, maternal compound genotype and child's compound genotype