A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference

Figure 1

Schematic of the data analysis pipeline used. To ensure that the highest quality alignments are created, reads are first filtered and then aligned to the human reference genome, hg19. Next, PCR duplicates are removed, reads are aligned around putative indels, and base quality scores are recalibrated. Finally, variants are called and validated against the NIST-GiaB list of variants.