RT Journal Article
SR Electronic
T1 MitoImpute: A Snakemake pipeline for imputation of mitochondrial genetic variants
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 649293
DO 10.1101/649293
A1 Tim W McInerney
A1 Brian Fulton-Howard
A1 Christopher Patterson
A1 Devashi Paliwal
A1 Lars S Jermiin
A1 Hardip R Patel
A1 Judy Pa
A1 Russell H Swerdlow
A1 Alison Goate
A1 Simon Easteal
A1 Shea J Andrews
A1 for the Alzheimer’s Disease Neuroimaging Initiative
YR 2019
UL http://biorxiv.org/content/early/2019/08/06/649293.abstract
AB Motivation Many available genotyping microarrays do not include sufficient mitochondrial single nucleotide variants (mtSNVs) to accurately assign sequences to their correct haplogroup. To address this, we created an easy to use mitochondrial DNA imputation pipeline, MitoImpute.Results We validated imputation accuracy by measuring haplogroup and genotype concordance in two datasets, 1000 Genomes Project and the Alzheimer’s Disease Neuroimaging Initiative. In both datasets, we observed a significant improvement in haplogroup concordance and excellent genotype concordance measures. We demonstrated that MitoImpute can be utilised by long-term studies whose older datasets have limited mtSNV genotypes, thus making them comparable with newer resequenced datasets.Availability https://github.com/sjfandrews/MitoImpute