Microarrays can be a cost-effective alternative to high-throughput sequencing for discovering novel single nucleotide polymorphisms (SNPs). Illumina’s iScan platform dominates the market, but their commercial microarray products are designed for model organisms. Further, the platform outputs data in a proprietary format. This cannot be easily converted to human-readable genotypes or be merged with pre-existing data. To address this, we present and validate a novel pipeline to facilitate data analysis from cross-species application of Illumina microarrays. This facilitates the generation of a compatible VCF from iScan data and the merging of this with a second VCF comprising genotypes derived from other samples and sources. Our pipeline includes a custom script, iScanVCFMerge (presented as a Python package), which we validate using iScan data from three great ape genera. We conclude that cross-species application of microarrays can be a rapid, cost-effective approach for SNP discovery in non-model organisms. Our pipeline surmounts the common challenges of integrating iScan genotypes with pre-existing data.

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Illumina iScan微阵列的跨物种应用可实现经济高效的高通量SNP发现

微阵列可以是发现新的单核苷酸多态性（SNP）的高通量测序的一种经济高效的选择。Illumina的iScan平台在市场上占主导地位，但其商业微阵列产品是为模型生物设计的。此外，平台以专有格式输出数据。不能轻易将其转换为人类可读的基因型或与现有数据合并。为了解决这个问题，我们提出并验证了一条新颖的流程，以促进从Illumina微阵列跨物种应用程序进行数据分析。这有助于从iScan数据生成兼容的VCF，并将其与包含其他样本和来源的基因型的第二VCF合并。我们的管道包括一个自定义脚本iScanVCFMerge（以Python软件包形式提供），我们使用来自三个大猿属的iScan数据进行了验证。我们得出结论，微阵列的跨物种应用可以是一种在非模式生物中发现SNP的快速，经济高效的方法。我们的产品线克服了将iScan基因型与现有数据整合在一起的常见挑战。