Genomic sequence variation analysis by resequencing

Abstract

Whole-genome resequencing is a method for determining the differences between individuals and a reference genome. The experiments are performed by sequencing the individuals, aligning generated reads to a common reference and discovering variation within the data set by analysis of the alignment with software tools. When correlated with phenotypic information, sites of causative genomic variation may be putatively assigned. While the analysis is generally straightforward, there are many nuances, and we aim to help you understand how to generate an initial result, sift through it to identify likely candidates for a phenotype of interest, and flag false positive calls.