This is a project which is currently making use of HPC facilities at Newcastle University. It is active.
For further information about this project, please contact:
High-quality, highly enriched mitochondrial DNA (mtDNA) sample enables detection of extremely low-frequency mtDNA variants. When mtDNA is carefully enriched, fragmented in the presence of EDTA and sequenced with unique dual indices by Illumina HiSeq in paired-end mode, it is possible to reliably detect variants at allele frequencies <0.05 %. To be able to detect variants at every position of the mtDNA genome, 'dual' alignment and variant calling strategy is required.
A pipline using Flexbar, BWA, SAMtools, BedTools, LoFreq+, & SnpEff to call and validate rare mtDNA sequence variants out of illumina data.
Student's PhD thesis - https://kups.ub.uni-koeln.de/7941/
Protocol IO page - https://www.protocols.io/view/low-frequency-variant-calling-from-high-quality-mt-kqdg3d6pl25z/v1
Example paper using the tool - https://doi.org/10.1093/nar/gky456