ArticleBioMed research international2014
Improved variant calling accuracy by merging replicates in whole-exome sequencing studies.
Article in BioMed research international, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- The impact of DNA input amount and DNA source on the performance of whole-exome sequencing in cancer epidemiology.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2015Trial
- Assessing the impact of sequencing platforms and analytical pipelines on whole-exome sequencing.Frontiers in genetics · 2024Article
- Relative Frequencies ofInternational journal of molecular sciences · 2022Review
- Comparison of GATK and DeepVariant by trio sequencing.Scientific reports · 2022Article
- RNA-SSNV: A Reliable Somatic Single Nucleotide Variant Identification Framework for Bulk RNA-Seq Data.Frontiers in genetics · 2022Article
- Evaluation of pathogenetic mutations in breast cancer predisposition genes in population-based studies conducted among Chinese women.Breast cancer research and treatment · 2020Article
- dCATCH-Seq: improved sequencing of large continuous genomic targets with double-hybridization.BMC genomics · 2017Article
- Mutations in C8ORF37 cause Bardet Biedl syndrome (BBS21).Human molecular genetics · 2016Article
- Replicate exome-sequencing in a multiple-generation family: improved interpretation of next-generation sequencing data.BMC genomics · 2015Article
- SCNVSim: somatic copy number variation and structure variation simulator.BMC bioinformatics · 2015Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
In large scale population-based whole-exome sequencing (WES) studies, there are some samples occasionally sequenced two or more times due to a variety of reasons. To investigate how to efficiently utilize these duplicated sequencing data, we conducted comprehensive evaluation of variant calling strategies. 92 samples subjected to WES twice were selected from a large population study. These 92 duplicated samples were divided into two groups: group H consisting of the higher sequencing depth for each subject and group L consisting of the lower depth for each subject. The merged samples for each subject were put in a third group M. Using the GATK multisample toolkit, we compared variant calling accuracy among three strategies. Hierarchical clustering analysis indicated that the two replicates for each subject showed high homogeneity. The comparative analyses on the basis of heterozygous-homozygous ratio (Hete/Homo), transition-transversion ratio (Ti/Tv), and overlapping rate with the 1000 Genomes Project consistently showed that the data quality of the SNPs detected from the M group was more accurate than that of SNPs detected from the H and L groups. These results suggested that merging homogeneous duplicated exomes instead of using one of them could improve variant calling accuracy.
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