TY - JOUR
T1 - MitoSAVE
T2 - Mitochondrial sequence analysis of variants in Excel
AU - King, Jonathan L.
AU - Sajantila, Antti
AU - Budowle, Bruce
N1 - Funding Information:
The authors would like to thank David Warshauer and Dixie Peters for constructive comments and critical review of the manuscript. This work was supported in part by award no. 2012-DN-BXK033 , awarded by the National Institute of Justice, Office of Justice Programs, U.S. Department of Justice . The opinions, findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect those of the U.S. Department of Justice. AS has been supported by Finnish Foundations’ Professor Pool ( Paulo Foundation ).
PY - 2014/9
Y1 - 2014/9
N2 - The mitochondrial genome (mtGenome) contains genetic information amenable to numerous applications such as medical research, population and evolutionary studies, and human identity testing. However, inconsistent nomenclature assignment makes haplotype comparison difficult and can lead to false exclusion of potentially useful profiles. Massively Parallel Sequencing (MPS) is a platform for sequencing large datasets and potentially whole populations with relative ease. However, the data generated are not easily parsed and interpreted. With this in mind, mitoSAVE has been developed to enable fast conversion of Variant Call Format (VCF) files. mitoSAVE is an Excel-based workbook that converts data within the VCF into mtDNA haplotypes using phylogenetically-established nomenclature as well as rule-based alignments consistent with current forensic standards. mitoSAVE is formatted for human mitochondrial genome; however, it can easily be adapted to support other reasonably small genomes.
AB - The mitochondrial genome (mtGenome) contains genetic information amenable to numerous applications such as medical research, population and evolutionary studies, and human identity testing. However, inconsistent nomenclature assignment makes haplotype comparison difficult and can lead to false exclusion of potentially useful profiles. Massively Parallel Sequencing (MPS) is a platform for sequencing large datasets and potentially whole populations with relative ease. However, the data generated are not easily parsed and interpreted. With this in mind, mitoSAVE has been developed to enable fast conversion of Variant Call Format (VCF) files. mitoSAVE is an Excel-based workbook that converts data within the VCF into mtDNA haplotypes using phylogenetically-established nomenclature as well as rule-based alignments consistent with current forensic standards. mitoSAVE is formatted for human mitochondrial genome; however, it can easily be adapted to support other reasonably small genomes.
KW - Bioinformatics
KW - Forensic nomenclature
KW - Massively Parallel Sequencing (MPS)
KW - Mitochondrial genome (mtGenome)
KW - Mitochondrial haplotype
KW - Variant Call Format (VCF) file
UR - http://www.scopus.com/inward/record.url?scp=84903214880&partnerID=8YFLogxK
U2 - 10.1016/j.fsigen.2014.05.013
DO - 10.1016/j.fsigen.2014.05.013
M3 - Article
C2 - 24952129
AN - SCOPUS:84903214880
SN - 1872-4973
VL - 12
SP - 122
EP - 125
JO - Forensic Science International: Genetics
JF - Forensic Science International: Genetics
ER -