Pedigree section

The Pedigree section displays relatedness metrics and the results of relationship validation for each pair of samples in the family tree.

Included metrics

Relatedness coefficient (observed)

Shows the observed coefficient of relatedness between sample pairs. The expected coefficient is available via hover tooltip for quick comparison.

IBS0

Identity by state 0—a number of genomic loci where two individuals share zero alleles. This occurs when the two individuals are opposite homozygotes for a biallelic SNP.

This metric is calculated across a set of biallelic SNPs and is inversely related to the degree of genetic similarity between the individuals. A low IBS0 count suggests a higher degree of overall genetic similarity, but it is an indirect and limited measure of genetic relatedness that requires interpretation alongside other metrics.

Relationship validation result

Summarizes the outcome of the relationship validation, confirming whether the observed data aligns with the expected pedigree structure.

Relationship validation calculation

Relationship validation is done by Peddy based on:

• Relatedness coefficient (𝑟)—a measure of how much two individuals share alleles from a common ancestor, indicating the probability that alleles at the same genome location are identical by descent

• IBS0 (Identity by state 0)—a number of genomic loci where two individuals share zero alleles, ie, they are opposite homozygotes

• IBS2 (Identity by state 2)—a number of genomic loci where two individuals share two alleles, meaning they have the exact same genotype

Peddy takes the inferred relationships from the genetic data and cross-references them against the declared relationships. For every pair of individuals in a cohort, Peddy calculates a coefficient of relatedness from the genotypes observed at the sampled sites.

For each possible pair of samples in a pedigree, the expected relatedness coefficient based on declared family relation is compared with the observed relatedness coefficient (𝑟). IBS0 value helps to differentiate between sibling and parent–child relationships, both expected to have ~50% relatedness coefficient (see table).

Inferred relationship	Expected IBS0 number	Expected 𝑟 (%)	Observed 𝑟 (%) and interpretation
Unrelated	Relatively high	0	< 0.2 Pass 0.2–4 Shared ancestry 4–15 Consanguinity > 15 Consanguinity + Failed validation
Parent–child	0 or close to 0. Any IBS0 sites—due to genotyping errors	50	< 40 Failed validation 40–60 Pass > 60 Failed validation
Full siblings	Small but detectable number	50	< 40 Failed validation 40–60 Pass > 60 Failed validation