GenoSeq: A genotyping tool for next-generation sequencing data in genome-wide association study

GenoSeq is a genotyping tool for next-generation sequencing data that enables users to obtain SNP genotype data from multiple samples of raw genome sequencing data in a convenient manner. To extract genotype data for genome-wide association study (GWAS), usually, raw genome sequencing data should pass through several stages. At each stage, user needs to make proper selection for many options about tools/algorithms and parameters. Moreover, the options made at each stage can lead to different genotyping results. In reality, it is not easy for users to select appropriate options without deep understanding of them. To handle this problem, in this paper, we introduce a new genotyping tool which is called GenoSeq. With this tool, users can perform a SNP genotyping procedure for next-generation sequencing data under a unified framework by automatically creating a series of several modular tasks (called process stream). Specifically, GenoSeq can produce genotype data for given SNP positions from multiple samples of raw genome sequencing data by following the recommended procedure. The pedigree file will be the final output of genotyping results, which is a typical input format for many GWAS tools.