Dreep Files

1) position_influenced_by_numt.csv includes all the positions on mtDNA that having at least one alternative NUMTs allele
2) NUMTs.list.csv includes all the NUMTs by BLASTN rCRS against HG19(without chrM). e_value threshold is 0.0001 (Hazkani-Covo et al. 2010 PloS Genet e1000834)
3) polymorphism_numt.csv shows all the polymorphic positions on mtDNA and whether the alternative allele was also observed as a NUMTs allele

If you want to have your own criteria (different e_value) to define NUMTs, run BLASTN first and run 
perl blast_numts_summary.pl [blast result] to have your own NUMTs.list.csv
or run
perl blast_result [blast result] to have your own position_influenced_by_numt.csv

If you know perl, you can also specify other parameters in the scripts. 

two perl modules are required: BIO::SearchIO BIO::Seq