Fig. 5
From: Impact of post-alignment processing in variant discovery from whole exome data
Change of known and novel SNP calls by BQSR in NA12878. a SNP calls from SAMtools in the non-HLA regions. b SNP calls from SAMtools in the HLA region. c SNP calls from Platypus in the non-HLA regions. d SNP calls from Platypus in the HLA region. NA12878 exome-seq data NA12878_04 (full, approximate 100x coverage; Additional file 2: Table S1) was down-sampled into 40, 20 and 10x coverage. Y-axis represents the difference in the number of SNPs, separated into known and novel, before and after BQSR. Negative number indicates missed calls after BQSR, compared to local realignment. Known SNPs are those that match dbSNP v138