CIGenotyper: A Machine Learning Approach for Genotyping Complex Indel Calls

Complex insertion and deletion (complex indel) is a rare category of genomic structural variations. A complex indel presents as one or multiple DNA fragments inserted into the genomic location where a deletion occurs. Several studies emphasize the importance of complex indels, and some state-of-the-art approaches are proposed to detect them from sequencing data. However, genotyping complex indel calls is another challenged computational problem because some commonly used features for genotyping indel calls from the sequencing data could be invalid due to the components of complex indels. Thus, in this article, we propose a machine learning approach, CIGenotyper to estimate genotypes of complex indel calls. CIGenotyper adopts a relevance vector machine (RVM) framework. For each candidate call, it first extracts a set of features from the candidate region, which usually includes the read depth, the variant allelic frequency for aligned contigs, the numbers of the splitting and discordant paired-end reads, etc. For a complex indel call, given its features to a trained RVM, the model outputs the genotype with highest likelihood. An algorithm is also proposed to train the RVM. We compare our approach to two popular approaches, Gindel and Pindel, on multiple groups of artificial datasets. The results of our model outperforms them on average success rates in most of the cases when vary the coverages of the given data, the read lengths and the distributions of the lengths of the pre-set complex indels.