Maria Zanti, Kyriaki Michailidou, Maria A Loizidou, Christina Machattou, Panagiota Pirpa, Kyproula Christodoulou, George M Spyrou, Kyriacos Kyriacou, Andreas Hadjisavvas
BACKGROUND: Next-generation sequencing (NGS) represents a significant advancement in clinical genetics. However, its use creates several technical, data interpretation and management challenges. It is essential to follow a consistent data analysis pipeline to achieve the highest possible accuracy and avoid false variant calls. Herein, we aimed to compare the performance of twenty-eight combinations of NGS data analysis pipeline compartments, including short-read mapping (BWA-MEM, Bowtie2, Stampy), variant calling (GATK-HaplotypeCaller, GATK-UnifiedGenotyper, SAMtools) and interval padding (null, 50 bp, 100 bp) methods, along with a commercially available pipeline (BWA Enrichment, Illumina®)...
April 28, 2021: BMC Bioinformatics