On genomic repeats and reproducibility
On genomic repeats and reproducibility
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DOI：
10.1093/bioinformatics/btw139
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发表时间：
2016-08-01
期刊：
影响因子：
5.8
通讯作者：
Alkan, Can
中科院分区：
文献类型：
--
作者：
Firtina, Can;Alkan, Can
结果如下：在这里，我们提出了一个全面的分析，使用高通量测序数据的基因组变异的计算表征的再现性。我们使用相同的工具和相同的参数对相同的数据集进行了两次重新分析，其中我们只改变了输入（即FASTQ文件）中的读取顺序。重排导致来自重复区域的读段在第二次比对中被映射到不同的位置，并且当我们仅应用分散/聚集方法进行读段映射时，我们观察到类似的结果，而没有预先重排。我们的研究结果表明，一些最常见的变异发现算法不处理模糊的读段映射时，随机位置的选择准确。此外，我们还观察到，即使使用完全相同的比对，GATK HaplotypeCaller也会生成略有不同的调用集，我们将其精确定位到变体过滤步骤。我们的结论是，算法在基因组变异发现和表征的每一步都需要以确定性的方式处理模糊映射，以确保结果的完全复制。可用性和实施：代码，脚本和生成的VCF文件可在DOI：10.5281/zenodo.32611。
Results: Here, we present a comprehensive analysis on the reproducibility of computational characterization of genomic variants using high throughput sequencing data. We reanalyzed the same datasets twice, using the same tools with the same parameters, where we only altered the order of reads in the input (i.e. FASTQ file). Reshuffling caused the reads from repetitive regions being mapped to different locations in the second alignment, and we observed similar results when we only applied a scatter/gather approach for read mapping-without prior shuffling. Our results show that, some of the most common variation discovery algorithms do not handle the ambiguous read mappings accurately when random locations are selected. In addition, we also observed that even when the exact same alignment is used, the GATK HaplotypeCaller generates slightly different call sets, which we pinpoint to the variant filtration step. We conclude that, algorithms at each step of genomic variation discovery and characterization need to treat ambiguous mappings in a deterministic fashion to ensure full replication of results.Availability and Implementation: Code, scripts and the generated VCF files are available at DOI: 10.5281/zenodo.32611.