상위피인용논문
- 조회1,032
Sohyun Hwang1,2,*, Eiru Kim2,*, Insuk Lee2,# & Edward M. Marcotte1,#
1Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, TX 78712, USA.
2Department of Biotechnology, Yonsei University, Seoul, 120-749, Korea.
*These authors contributed equally to this work.
#Corresponding author
Abstract
The success of clinical genomics using next generation sequencing (NGS) requires the accurate and consistent identification of personal genome variants. Assorted variant calling methods have been developed, which show low concordance between their calls. Hence, a systematic comparison of the variant callers could give important guidance to NGS-based clinical genomics. Recently, a set of high-confident variant calls for one individual (NA12878) has been published by the Genome in a Bottle (GIAB) consortium, enabling performance benchmarking of different variant calling pipelines. Based on the gold standard reference variant calls from GIAB, we compared the performance of thirteen variant calling pipelines, testing combinations of three read aligners—BWA-MEM, Bowtie2 and Novoalign—and four variant callers—Genome Analysis Tool Kit HaplotypeCaller (GATK-HC), Samtools mpileup, Freebayes and Ion Proton Variant Caller (TVC), for twelve data sets for the NA12878 genome sequenced by different platforms including Illumina2000, Illumina2500 and Ion Proton, with various exome capture systems and exome coverage. We observed different biases toward specific types of SNP genotyping errors by the different variant callers. The results of our study provide useful guidelines for reliable variant identification from deep sequencing of personal genomes.
논문정보
- Research article
- 2015년 12월 (BRIC 등록일 2020-05-26)
- 국내(교신)+국외 연구진
- 생명과학 > 유전학
- 120회 이상 인용된 논문
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