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Variant Phasing

The Whole Genome Sequencing app performs pedigree-backed phasing on the proband sample if the pedigree includes proband and both parents. This captures information about whether a given allele in the proband was inherited maternally or paternally. For the parent it captures which allele was transmitted to the proband. Phasing information can be useful for evaluating pairs or groups of variants, such as compound heterozygotes. The phasing representation in the genotype field of the proband VCF is "maternal allele | paternal allele" and the phasing representation in the genotype field of the parent VCF is "proband allele | other allele".

Table 1   Example genoptype fields

Mother	Father	Child
0 | 0	1 | 1	0 | 1
1 | 1	0 | 1	1 | 0
2 | 1	1 | 0	2 | 1
0 | 0	1 | 0	0 | 1
1 | 0	0	1 | 0
0 | 1	1	0 | 1
1 | 0	1	1
0 | 1	0	0
1 | 0	1 | 1	1 | 1
1 | 0	1 | 0	1 | 1

Table 2   Example genotypes that are not phased

Mother	Father	Child
0 / 1	0 / 1	0 / 1

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