TABLE 1.

A descriptive summary of mtDNA variant callers selected for comparative analyses.

Features	Mutserve v1.1.17	MitoSeek v1.3	mitoCaller v1.0	MToolBox v1.2	GATK v3.7 and v4.2- HaplotypeCaller
	Version from 19/02/19	Version from 13/05/2019	Version from 16/01/2018	Version from 15/11/2021	Versions from 12/12/2016 and 18/0/2021
Process Location	Local, command line	Local, command line	Local, command line	Local, command line	Local, command line
Input File format	BAM	BAM	BAM	BAM	BAM
Mitochondrial alignment	rCRS mitochondrial reference	rCRS mitochondrial reference	“double alignment” strategy, with rCRS mitochondrial reference and a shifted rCRS reference	RSRS and rCRS mitochondrial reference	rCRS mitochondrial reference
Heteroplasmic variant detection	Yes	Yes	Yes	Yes	Yes
Homoplasmic variant detection	Yes	No	Yes	Yes	Yes
Default heteroplasmic threshold	1%	5%	Based on likelihood model	20%	Based on likelihood model
Altering heteroplasmic threshold	--level parameter	-hp parameter	a custom script for threshold detection was used in the study	hf_min parameter in config file	a custom script for threshold detection was used in the study
Description of the variant-calling algorithm	Maximum likelihood model for detecting heteroplasmic variants	One-tail Fisher’s exact test for detecting heteroplasmic variants	Maximum likelihood-based model for both heteroplasmic and homoplasmic variants detection	Identification of mismatches in the newly assembled mitochondrial genome (or differences in the SAM CIGAR string for INDELs)	Bayesian model for both heteroplasmic and homoplasmic variants detection