TY - GEN
T1 - Integrated genotyping of structural variation
AU - Fan, Xian
AU - Nakhleh, Luay
AU - Chen, Ken
N1 - Copyright:
Copyright 2014 Elsevier B.V., All rights reserved.
PY - 2013
Y1 - 2013
N2 - Discovering genotype of structural variations (SV) is a new and challenging topic. To the best of our knowledge, estimation of variant allele frequency (VAF) of an SV from both read depth and read alignment has not been done. In this study, we propose BreakDown, a new statistical model that integrates read depth, discordant and split paired-end read alignment to accurately estimate SVs' genotypes and VAFs. Application to 43 low coverage samples in the 1000 Genomes Project shows that BreakDown produces highly accurate genotypes, especially on heterozygous deletions. Estimation of VAFs on both low- and high-coverage data is shown to converge on expected values with small divergence.
AB - Discovering genotype of structural variations (SV) is a new and challenging topic. To the best of our knowledge, estimation of variant allele frequency (VAF) of an SV from both read depth and read alignment has not been done. In this study, we propose BreakDown, a new statistical model that integrates read depth, discordant and split paired-end read alignment to accurately estimate SVs' genotypes and VAFs. Application to 43 low coverage samples in the 1000 Genomes Project shows that BreakDown produces highly accurate genotypes, especially on heterozygous deletions. Estimation of VAFs on both low- and high-coverage data is shown to converge on expected values with small divergence.
UR - http://www.scopus.com/inward/record.url?scp=84897704417&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84897704417&partnerID=8YFLogxK
U2 - 10.1109/GlobalSIP.2013.6736808
DO - 10.1109/GlobalSIP.2013.6736808
M3 - Conference contribution
AN - SCOPUS:84897704417
SN - 9781479902484
T3 - 2013 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2013 - Proceedings
SP - 47
EP - 48
BT - 2013 IEEE Global Conference on Signal and Information Processing, GlobalSIP 2013 - Proceedings
T2 - 2013 1st IEEE Global Conference on Signal and Information Processing, GlobalSIP 2013
Y2 - 3 December 2013 through 5 December 2013
ER -