Figure 2.

Overview of the variant calling pipeline. VCP consists of sequence analysis software and in-house built algorithms, and its output gives a wide variety of sequencing results. Sequence reads are first filtered for quality. Sequence alignment is then performed with BWA, followed by duplicate removal, variant calling with SAMtools' pileup and in-house developed algorithms for SNV calling with qualities and REA calling. File transformation programs are used to convert different file formats between the software. White boxes, files and intermediate data; purple boxes, filtering steps; grey ellipses, software and algorithms; green boxes, final VCP output; yellow boxes, files for data visualization; area circled with blue dashed line, VCP analysis options not used in this study. PE, paired end.