GenoSeq A genotyping tool for nextgeneration seq

Authors: Jinwoo Kim Jaeyoung Kim Miyoung Shin

Publish Date: 2013/12/20

Volume: 7, Issue: 4, Pages: 353-360

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Abstract

GenoSeq is a genotyping tool for nextgeneration 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 genomewide 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 nextgeneration 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

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