Challenges in exome analysis by LifeScope and its alternative computational pipelines

BMC Research Notes
Erinija PranckevičieneVaidutis Kučinskas

Abstract

Every next generation sequencing (NGS) platform relies on proprietary and open source computational tools to analyze sequencing data. NGS tools for Illumina platforms are well documented which is not the case with AB SOLiD systems. We applied several computational and variant calling pipelines to analyse targeted exome sequencing data obtained using AB SOLiD 5500 system. Our investigated tools comprised proprietary LifeScope's pipeline in combination with open source color-space competent mapping programs and a variant caller. We present instrumental details of the pipelines that were used and quantitative comparative analysis of variant lists generated by LifeScope's pipeline versus open source tools. Sufficient coverage of targeted regions was achieved by all investigated pipelines. High variability was observed in identities of variants across the mapping programs. We observed less than 50% concordance of variant lists produced by approaches based on different mapping algorithms. We summarized different approaches with regards to coverage (DP) and quality (QUAL) properties of the variants provided by GATK and found that LifeScope's computational pipeline is superior. Fusion of information on mapping profiles (pileup) at geno...Continue Reading

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Citations

Jun 9, 2017·Journal of Clinical Laboratory Analysis·Viktoria SzabadosovaIvan Bernasovsky
Dec 7, 2018·JCI Insight·Anika WehrleEkkehart Lausch

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Methods Mentioned

BETA
exome sequencing

Software Mentioned

Lifescope
LITGEN
T RealignerTargetCreator
FastQC
csfasta
Bfast
SortSam
SAET
like Fast Accurate Search Tool ( BFAST )
AddOrReplaceReadGroups

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