Challenges in exome analysis by LifeScope and its alternative computational pipelines

摘要: Every next generation sequencing (NGS) platform relies on proprietary and open source computational tools to analyze data. NGS for Illumina platforms are well documented which is not the case with AB SOLiD systems. We applied several variant calling pipelines analyse targeted exome data obtained using 5500 system. Our investigated comprised LifeScope’s pipeline in combination color-space competent mapping programs a caller. present instrumental details of that were used quantitative comparative analysis lists generated by versus tools. Sufficient coverage regions was achieved all pipelines. High variability observed identities variants across programs. less than 50 % concordance produced approaches based different algorithms. summarized regards (DP) quality (QUAL) properties provided GATK found superior. Fusion information profiles (pileup) at genomic positions alignments proved be useful strategy assess questionable singleton variants. quantitatively supported conclusion Lifescope’s superior processing Nevertheless use alternative encouraged because aggregation from other helps resolve calls increases confidence call. It noted threshold considered further has chosen data-driven way prevent loss important information.