CONTRA: copy number analysis for targeted resequencing
CONTRA: copy number analysis for targeted resequencing
复制标题
DOI：
10.1093/bioinformatics/bts146
复制
发表时间：
2012-05-15
期刊：
影响因子：
5.8
通讯作者：
Gorringe, Kylie L.
中科院分区：
文献类型：
--
作者：
Li, Jason;Lupat, Richard;Gorringe, Kylie L.
结果：我们提出了一种检测TR数据CNV的方法，包括全外显子组捕获数据。我们的方法调用基于标准化覆盖深度的每个目标区域的拷贝数增益和损失。我们的主要策略包括使用基本水平的对数比来消除gc含量偏差，纠正不平衡的库大小对对数比的影响，以及通过分组和插值来估计对数比的变化。我们的方法可通过CONTRA （COpy Number Targeted Resequencing Analysis）获得，CONTRA是一个软件包，采用标准比对格式（BAM/SAM），输出变体调用格式（VCF4.0），便于与其他下一代测序分析软件包集成。我们使用来自7种不同的靶细胞富集试验的样本来评估我们的方法，并使用模拟数据和已知CNV基因型的真实种系数据来评估我们的结果。
Results: We present a method for CNV detection for TR data, including whole-exome capture data. Our method calls copy number gains and losses for each target region based on normalized depth of coverage. Our key strategies include the use of base-level log-ratios to remove GC-content bias, correction for an imbalanced library size effect on log-ratios, and the estimation of log-ratio variations via binning and interpolation. Our methods are made available via CONTRA (COpy Number Targeted Resequencing Analysis), a software package that takes standard alignment formats (BAM/SAM) and outputs in variant call format (VCF4.0), for easy integration with other next-generation sequencing analysis packages. We assessed our methods using samples from seven different target enrichment assays, and evaluated our results using simulated data and real germline data with known CNV genotypes.