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added two bowtie2 numbers for comparison

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Heng Li 2017-11-02 15:44:48 -04:00
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@ -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}