Variant Calling and Microarray Expression Analysis in Pancreatic Islet Samples

Sammanfattning: Abstract This article describes the creation of a pipeline for variant calling from high-throughput next-generation exome and RNA sequencing data using commonly used bioinformatics tools. High-throughput sequencing data from six pancreatic islet cell samples were analyzed using the pipeline, and the resulting variant calls were validated against chip genotyping data from the same individuals. The results indicate that variant calling can be applied to RNA-seq and exome sequencing data to identify genetic variants in exons and coding regions with high precision, while the recall was relatively low. In other words, identified genotypes seem to have a high probability of being correct, but only part of the present variants are picked up. This is especially true for RNA-seq.