Fig. 1
From: Similarities and differences between variants called with human reference genome HG19 or HG38
Study design. Whole genome sequencing data from GIAB reference sample NA12878 was downloaded and aligned to human genomes HG19 and HG38 using three aligners followed by SNVs calling using various calling algorithms. The SNVs were then converted between the two reference genomes using Picard and CrossMap. To pinpoint discordant SNVs, converted SNVs were compared against SNVs identified by directly using the target reference genome version. Finally, discordant SNVs were characterized by read depth, low-confidence frequency and prevalence of G/C reference alleles