NUMTS analysis

Based on the work of: https://github.com/WeiWei060512/NUMTs-detection 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

Consists of:

* *Analysis*  
* *Methods*  
  
To detect NUMTs, we used the aligned WGS BAM files and extracted the discordant read pairs  
using samblaster and samtools and included the read pairs where one end aligns to nuclear genome  
and the other end aligns to the mtDNA reference sequence. The reads with mapping quality higher  
than 0 were used. The discordant reads were then clustered together based on sharing the same  
orientation and whether they were within a distance of 500 bp. We detected the clusters  
supported by at least two pairs of discordant reads. The NUMTs within a distance of 500bp  
on both nuclear DNA and mtDNA were grouped as the same NUMT.  
We found the NUMTs supported by at least two pairs of discordant reads. 


* *Data extraction*  
* *Visualization*  
	* Plots  
	* Circos