NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types.
NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types.
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NGSCheckMate：用于在下一代测序研究中验证数据类型内和跨数据类型的样本身份的软件。
DOI：
10.1093/nar/gkx193
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发表时间：
2017-06-20
影响因子：
14.9
通讯作者：
Park PJ
中科院分区：
文献类型：
--
作者：
Lee S;Lee S;Ouellette S;Park WY;Lee EA;Park PJ
在许多下一代测序（NGS）研究中，针对每个个体分析多个样本或数据类型。这些研究中的一个重要质量控制（QC）步骤是确保来自同一受试者的数据集正确配对。考虑到多维研究中数据类型、文件类型和测序深度的异质性，提供用于基因型比较的标准化度量的稳健程序将是有用的。在这里，我们描述了NGSCheckMate，一个用户友好的软件包，用于验证样品的身份从FASTQ，BAM或VCF文件。该工具使用基于模型的方法来比较已知单核苷酸多态性的等位基因读段分数，考虑相同和不相关样本的相似性度量的深度依赖行为。我们的评估表明，NGSCheckMate适用于多种数据类型，包括外显子组测序、全基因组测序、RNA-seq、ChIP-seq、靶向测序和单细胞全基因组测序，对测序深度的要求最低（>0.5X）。可以直接在FASTQ文件上运行一个免安装模块，以进行快速的初始检查。我们建议在NGS研究中使用此软件作为QC步骤。可用性：https://github.com/parklab/NGSCheckMate
In many next-generation sequencing (NGS) studies, multiple samples or data types are profiled for each individual. An important quality control (QC) step in these studies is to ensure that datasets from the same subject are properly paired. Given the heterogeneity of data types, file types and sequencing depths in a multi-dimensional study, a robust program that provides a standardized metric for genotype comparisons would be useful. Here, we describe NGSCheckMate, a user-friendly software package for verifying sample identities from FASTQ, BAM or VCF files. This tool uses a model-based method to compare allele read fractions at known single-nucleotide polymorphisms, considering depth-dependent behavior of similarity metrics for identical and unrelated samples. Our evaluation shows that NGSCheckMate is effective for a variety of data types, including exome sequencing, whole-genome sequencing, RNA-seq, ChIP-seq, targeted sequencing and single-cell whole-genome sequencing, with a minimal requirement for sequencing depth (>0.5X). An alignment-free module can be run directly on FASTQ files for a quick initial check. We recommend using this software as a QC step in NGS studies. Availability: https://github.com/parklab/NGSCheckMate