Whole genome sequencing has revolutionized the study of genetics, and we are challenged with the task of extracting information from immense datasets in a simple, efficient and timely manner. Given the rapid decline in sequencing costs, genotyping-by-sequencing is now accessible to even small genetics projects, yet the bioinformatics and computing resources involved can be daunting if not prohibitive for some laboratories.   

Here we present ArrayMaker, a user-friendly tool which extracts accurate single nucleotide polymorphism (SNP) genotypes from whole genome sequence alignments. SNP genotypes are output in a standard format compatible with both association analysis software and datasets genotyped on commercial array platforms. The application is initiated by a single Linux command. It requires no installation and has a single dependency, SAMtools¹.

ArrayMaker enables geneticists with any level of computing expertise to quickly and easily genotype aligned samples at any desired list of markers, facilitating genome wide association analysis, fine mapping, candidate variant assessment, data sharing and compatibility of data sourced from multiple technologies.