Evaluation of Whole-Genome Sequencing of Four Chinese Crested Dogs for Variant Detection Using the Ion Proton System. Whole Genome Sequencing with Ion Proton System

In this study we have performed whole-genome re-sequencing of four Chinese Crested dogs. For each dog one sequencing library was prepared and sequenced on two Ion PI™ chips Kit v2 and sequenced on the Ion Proton™ System using Ion PI™ Sequencing 200 Kit v2 chemistry (200 bp read length, Life Technologies). On average, one chip yielded 73.3 million reads with a mean read length of 130 bp (~9.5 Gb sequence data). Reads were aligned to the canine reference genome sequence CanFam3.1. using TorrentSuit 3.6 software with default settings. Obtained BAM files further processed by marking and removing duplicate reads, recalibrating base quality scores and realigning INDELs. Single Nucleotide Polymorphisms where called with two variant calling tools: SAMtools and GATK UnifiedGenotyper tool. Raw variants filtered and both files merged together resulting in 4.83 million SNP in Chinese Crested dogs.