IBDelphi - Algorithm

The algorithm consists of the following 8 steps:

1. Read data in the first genotype data file and create an ordered list of the SNPs in this file, sorted by chromosome and position.

2. Add the genotype data of both individuals to this list of SNPs

3. Delete any SNPs that has a 'NoCall' or is missing genotype data for either of the individuals.

4. Identify heterozygous SNP genotypes in extended runs of homozygous SNP. Since these are probably miss-called genotypes they are also deleted.

5. Identify extended regions that do not contain SNPs that are homozygous in both individuals, but for different allele (i.e. he is 'AA' and she is 'BB'), these regions are probably Identical By Descent.

6. Scan the regions found in step 5 for extended runs that do not contain SNPs that are heterozygous in only one individual (i.e. he is 'AB' and she is 'BB'). These regions may be Identical By Descent for both chromosomes.

7. Identify extended runs of homozygosity in the individual's genomes.

8. Determine the genomic length of the Identical By Descent regions and calculate the proportions of the genome that is Identical By Descent in the two individuals. If either of the individuals has extended homozygous regions, recalculate this value excluding the homozygous regions since it is unlikely that either individual is homozygous for a disease bearing haplotype.