2.4. Identical by Descent Analysis

Identity by descent (IBD) was conducted by applying an algorithm described by Pagnamenta et al. [27], without the need to lift-over the genome version or downsampling SNP counts. A multi-sample VCF file with all sequenced family members was filtered by applying the following set of filters: a reads depth of >14, genotype quality of >30, no mendelian error, and an allelic ratio difference of >0. Next, a pair-wise analysis between all affected patients was performed. For each Single-Nucleotide Variant (SNV) in each pair, the absolute difference between the ratios of alternative variant read count and read depth was taken:

where A denotes the current site, 1 or 2—patient from pair, AD—alternative variant read count (allelic depth), and DP—read depth.

Finally, pairs with identical genotypes were filtered out as a non-informative.