Computationally Characterizing Genomic Pipelines Using High-confident Call Sets

In this paper, we describe some available high-confident call sets that have been developed to test the accuracy of called single nucleotide polymorphisms (SNPs) from next-generation sequencing. We use these calls to test and parameterize the GATK best practice pipeline on the computing cluster at the University of Kentucky. Automated scripts to run the pipeline can be found at https://github.com/sallyrose0425/GATKBP. This study demonstrates the usefulness of high-confident call sets in validating and optimizing bioinformatics pipelines, estimates computational needs for genomic analysis, and provides scripts for an automated GATK best practices pipeline.