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Table 3 Mendelian concordance of SV genotyping methods on trio datasets

From: Comprehensive evaluation of structural variant genotyping methods based on long-read sequencing data

SV genotyping method MCR
HG002 Tier 1 HG002 Tier 2 HG005
cuteSV 0.92 0.83 0.95
LRcaller 0.98 0.96 0.98
Sniffles 0.91 0.92 0.94
SVJedi 0.97 0.96 0.97
VaPoR 0.95 0.92 0.96
  1. The Ashkenazim trio includes son HG002, father HG003, and mother HG004. The Chinese trio includes son HG005, father HG006, and mother HG007. Performance was estimated based on ~ 30× PacBio CLR data. The alignment files were from minimap2 because its output was compatible with all SV genotyping methods
  2. MCR Mendelian concordance rate
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BMC Genomics

ISSN: 1471-2164

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