From a9790c0f1d964fd80a1edd2f97bbd50df9eb0bce Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 2 Nov 2017 15:44:48 -0400 Subject: [PATCH] added two bowtie2 numbers for comparison --- tex/minimap2.tex | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/tex/minimap2.tex b/tex/minimap2.tex index b14baac..cfb19ed 100644 --- a/tex/minimap2.tex +++ b/tex/minimap2.tex @@ -543,16 +543,17 @@ in minimap2 in future. To evaluate the accuracy of minimap2 on real data, we aligned human reads (AC:ERR1341796) with BWA-MEM and minimap2, and called SNPs and small INDELs with GATK HaplotypeCaller v3.5~\citep{Depristo:2011vn}. This run was sequenced -from experimentally mixed CHM1 and CHM13 cell lines. Both them are homozygous +from experimentally mixed CHM1 and CHM13 cell lines. Both of them are homozygous across the whole genome and have been \emph{de novo} assembled with SMRT reads -to high quality. This allowed us to construct an independent truth variant +to high quality. This allowed us to construct an independent truth variant data set (\href{https://github.com/lh3/CHM-eval}{https://github.com/lh3/CHM-eval}) for ERR1341796. In this evaluation, minimap2 has higher SNP false negative rate (FNR; 2.5\% of minimap2 vs 2.2\% of BWA-MEM), but fewer false positive SNPs per -million bases (FPPM; 3.0 vs 3.9), lower INDEL FNR (7.3\% vs 7.5\%) and similar -INDEL FPPM (both 1.0). The difference between the two mappers is much smaller -than between BWA-MEM and Bowtie2. +million bases (FPPM; 3.0 vs 3.9), lower 2--50bp INDEL FNR (7.3\% vs 7.5\%) and +similar INDEL FPPM (both 1.0). In comparison, Bowtie2 has a SNP FNR of 4.7\% +and INDEL FNR of 10.4\%. Minimap2 is broadly similar to BWA-MEM in the context +of small variant calling. \section{Conclusion}