This repository contains scripts for data processing and analysis used in the publication:
Wei W, Schon K, Elgar G, Orioli A, Tanguy M, Giess A, Tischkowitz M, Caulfield M, Chinnery PF. Nuclear-embedded mitochondrial DNA sequences in 66,083 human genomes. Nature 611, 105–114 (2022). https://doi.org/10.1038/s41586-022-05288-7
Note: It's not a software to do general analysis and won't be maintained. If you do use the code in your publications, please cite our paper.
NUMTs_detection.sh
searchBreakpoint_fromblatoutputs.py
searchNumtCluster_fromDiscordantReads.py
groupNumtCluster_fromMultipleSamples.py
enrichment_creatingRefgenome.py
enrichment_simulation.py
mtVariantCalling.sh
mtVariantCalling_MToolBox.conf
nanopolish_methylationDetection.sh
VarDetection_fromDiscSplitReads.sh
generateVariantTable.Human.py
generateVariantTable.HumanChimp.py
circos_allNUMTs.conf
confs
Whole genome sequence data that support the findings of this study can be analysed on the Genomics England data warehouse through https://www.genomicsengland.co.uk/understanding-genomics/data/