Illustration of input files.

Abstract

<p>A.) Pedigree structure. B.) Pedigree structure file storing the pedigree structure shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003880#pcbi-1003880-g002" target="_blank">Fig. 2A</a>. From the left-most column to the right-most column, the data are ID, mID (mother ID), fID (father ID), gender and sample name. C.) Part of VCF file. From the VCF file, we can find that the genome of the grandfather (G-Father) was not sequenced. We add his information to the pedigree structure file to avoid ambiguity. For example, if we include only one parent of two siblings in the pedigree structure file, it will be unclear whether they are full or half siblings. The sample name in the pedigree structure file should be the same as the sample name in the VCF file. When the actual genome was not sequenced, we set the corresponding sample name as NA in the pedigree structure file.</p