Following base quality recalibration, indel realignment and unified genotyper, the single-nucleotide variants were filtered for the removal of low-quality variant calls with GATK's VariantFiltrationWalker tool.
PCR duplicates were removed using Picard v.1.92, and base quality recalibration, indel realignment and single nucleotide polymorphism (SNP) and indel discovery were performed using the Genome Analysis Toolkit (GATK v.2.5-2).
We then repeated base-quality recalibration and realignment on the whole filtered set of variants on the two parents and all 70 RILs.
However, if the InDel is incorrect in the primary alignment (possibly due to chimeric read fragments, structural variations and/or misassemblies due to a poor-quality reference genome), InDel realignment may incorrectly realign the read segments surrounding the InDel.
Such steps include local realignment, base quality score recalibration, base alignment quality recalibration (BAQ), and removal of duplicate reads.
The sequencing reads were aligned to the reference genome using BWA [ 24], then preprocessed according to Broad best practice guidance (indel realignment, base quality score recalibration, and base alignment quality scoring).
Base quality recalibration and local realignment were carried out using Genome Analysis Toolkit (GATK) [ 17, 27].
(20) Genome Analysis Toolkit(21) was used for local realignment and quality score recalibration.
We then marked duplicates with Picard and carried out regional realignment and quality score recalibration using the Genome Analysis Toolkit (GATK) [ 1].
We then marked duplicates with Picard [ 17] and carried out regional realignment and quality score recalibration using Genome Analysis Toolkit (GATK) [ 18].
