A Bioinformatics pipeline for variant discovery from Targeted Next Generation Sequencing of the human mitochondrial genome



Lakshika Jayasekera, Kanchana Senanayake, Ruwandi Ranasinghe, Kamani Tennekoon

Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Sri Lanka

Competing interests: LJ none; KS none; RR none; KT none

Jayasekera et al. (2022) EMBnet.journal 28, e1007 http://dx.doi.org/10.14806/ej.28.0.1007

Received: 12 May 2021 Accepted: 23 September 2021 Published: 30 September 2022


Sequence variants of human mitochondrial DNA (mt DNA) have been implicated in a variety of disorders and conditions. Massive parallel sequencing is becoming increasingly popular due to its efficiency and cost-effectiveness. In relation to acquiring significant sequence information like levels of heteroplasmy in mt DNA, it offers a marked improvement compared to previous methods used. Here we describe a variant calling pipeline for human mitochondrial DNA using Next Generation Sequencing (NGS) data obtained by enriching the sample only for mitochondria prior to sequencing.


Human Mitochondrial (mt) genome is a double-stranded and a closed circular DNA molecule of 16,569 base pairs that represent <1% of total cellular DNA with each mitochondrion harboring 2-10 copies of mitochondrial DNA (mtDNA) molecules (Holt et al., 2007; Veltri et al., 1990). It codes for a total of 37 genes, including the 13 involved in electron transport and oxidative phosphorylation, 2 coding for 16rRNA and 12sRNA, and 22 coding for other mitochondrial transfer RNAs (tRNAs) needed for protein translation, thus proving its essential role in cellular function. (Anderson et al., 1981). The presence of dissimilar sequences across different mitochondrial DNA molecules, from a single source, is referred to as heteroplasmy, which could conform to varying degrees among several tissues or different cells of the same tissue (Melton, 2004; Wong et al., 2005). Compared to the nuclear genome, the mt genome has approximately 10 times higher mutation accumulation rate (Elmore, 2007), and it causes maternally inherited mitochondrial dysfunctions in a range of diverse disorders (mtDNA diseases) including diabetes mellitus, hypertension, Alzheimer’s disease, heart diseases and cancer (Huang, 2011). There’s also increasing evidence suggesting the association of somatic variants of mtDNA to other traits like ageing and cancer (Schon et al., 2012). Thus, the characterisation of mitochondrial genome sequences is necessary for the molecular diagnosis of associated conditions. However, mtDNA analyses methods like PCR-restriction fragment length polymorphism (PCR-RFLP) analyses, Affymetrix’s MitoChip, and even the gold standard Sanger sequencing fail to detect heteroplasmy under 10% (Mertens et al., 2019). Further, these methods are hindered by the limited number of targets they can scan in a single run, highlighting the need for an accurate, cost-effective, and more sensitive method to study mtDNA.

Next Generation Sequencing and mtDNA analysis

Massive parallel sequencing has revolutionised the sequencing technology in recent years and proves ideal for small genome sequencing due to its high throughput and low cost (Yao et al., 2019). Level of heteroplasmy detection could be significantly improved through these methods due to resulting high coverage and small size of the human mitochondrial genome. Although the different NGS technologies may use different methods in generating raw data, their final output is nucleotide base calls producing a huge number of 50 – 300 bp short reads (Mardis, 2013), usually combined in a FATSQ file.

Bioinformatics pipelines are an intrinsic aspect of NGS data analysis, to detect genomic alterations derived from these massive amounts of raw sequence data. The computationally intensive and complex nature of NGS data analysis makes many biologists who lack understanding of these computational techniques shy away from personally analysing raw sequence data (Roy et al., 2018). Several options are available to facilitate the analysis of mtDNA data acquired through NGS. However, their use is constrained by various factors. For example, several available bioinformatics pipeline frameworks like MitoSeek, Mtoolbox, are difficult to install, certain online servers like mit-o-matic, have limited input volumes or generate unreliable results (Weissensteiner et al., 2016) In this paper, we present a bioinformatics pipeline for analyzing NGS data of targeted sequencing of the mitochondrial genome, through a series of command line tools.


Quality assessment

When compared with Sanger sequencing, NGS acquire more errors as platforms face a variety of failures in chemistry and instrumentation, resulting in errors such as adaptor contamination, low-quality reads, and base call errors. To assure the conclusions derived through analysis are correct, it is necessary to eliminate these errors as downstream procedures fail to identify them (Pabinger et al., 2014; Cox et al., 2010; Dohm et al., 2008). In this protocol, FastQC (version 0.11.8) (Andrews, 2010), the most preferred tool among the several tools available for checking the quality of raw data, was used for quality assessment. Upon assessment, this tool produces a report of useful information including quality score distribution across bases and across reads. Base quality score is an expression of base calling accuracy (Zhou and Rokas, 2014). A score of >20 is commonly referred to as the threshold for inclusion criteria of sequence reads, and removing sequences lower than 20 is preferable. As a part of the quality control procedure, adaptor sequences and the sequences not meeting the defined standards were removed using the cutadapt (version 1.18) tool (Martin, 2011). Similarly, sequences that were significantly shorter and longer than average were removed as well.


Alignment is the process where the previously quality controlled massive amount of short reads, usually around 250 bp in FASTQ format, is mapped to the reference sequence that’s in FASTA format, in this scenario, rCRS Human Mitochondrial Genome Reference sequence of Genbank accession No. NC_012920.1 (Andrews et al.,1999). It is the paramount step of any variant calling pipeline as even a few inaccurate alignments could produce many false-positive variant calls. For the current pipeline, the BWA-MEM tool of BWA aligner (version 0.7.12, one of the popular aligners that is fast and facilitates indel identification, -r1039) was used (Li, 2013). BWA was also used for the indexing of the reference sequence that was downloaded from Genbank prior to alignment, and the resulting sequence alignment mapping (SAM) format file from the alignment between the reference sequence and trimmed sequences was converted to a binary alignment map (BAM) file using SAMtools (version 1.9) BAM is the default binary format for storing sequence alignment data (Li et al., 2009). Once the aligned BAM file is produced, alignment should be further refined. Accordingly, sorting and indexing of the BAM was also performed using SAMtools (version 1.9), through which BAM data is efficiently arranged and coordinate sorted, so the reads could be retrieved efficiently during further downstream analysis. SAMtools also compresses the aligned BAM file further before being used in deduplication (Li et al., 2009).

Removing/marking duplicates

Duplicate removal is also enabled through SAMtools (version 1.9). This additional refinement process is important to mitigate the effects generated by the over-amplification of certain sequences. Duplicate sequences that are naturally present spanning the interested regions on DNA do not need to be removed. However, optical duplicates that are mistakenly read as separate clusters through signal capture software, when in reality they are generated by the same cluster, and the duplicates caused through PCR should be removed. PCR duplicates occur when the same amplified copies of one original fragment are identified as different fragments and further amplified through high throughput sequencing (Zhou and Rokas, 2014). In the initial steps of the NGS process, mtDNA is fragmented for library preparation and amplified for enrichment. Therefore, the presence of PCR duplicates at some level is usual. But having overly propagated duplicates cause erroneous end results. If a sequence subjected to PCR duplication contains a variant, that variant call would be biased. To further worsen the final output, if an error had occurred during PCR it would be further inflated during high throughput sequencing and cause a false positive. Therefore, compared with other DNA sequencing projects, the effect of duplicates is detrimental for heteroplasmy level detection of mtDNA analysis. Through deduplication algorithms, the groups of duplicate reads are identified and that of the highest sum of base quality scores is marked as a single read (Goto, 2011; Pfeifer, 2017).

Base quality score recalibration

The last stage that produces the final output of variant calling is possible through several different software tools. Just as many tools applied in different stages of the analysis, no single software could perfectly identify all variants in the genome of interest without false positives or negatives, however, according to a survey of variant analysis tools previously performed (Pabinger et al., 2014), Genome Analysis Tool Kit (GATK) by Broad Institute of Harvard and MIT (McKenna et al., 2010; Heldenbrand et al., 2019) offers a satisfactory output for both germline and somatic variant calling. Prior to variant calling, Indel realignment and Base quality recalibration is the recommended practice. In previous versions of GATK, local alignment tools like IndelRealigner were available for Indel realignment. However, in the current version, GATK 4 realignment is no longer recommended (Heldenbrand et al., 2019). As per the GATK best practices pipeline (Van der Auwera et al., 2013), before the input files are processed through GATK tools, they should be preprocessed with utility software. Accordingly, a sequence dictionary for the reference file is created using CreateSequenceDictioanry tool by Picard (version 2.25.1), whereas the read group information of the input BAM file is assigned using the AddOrReplaceReadGroups tool also by Picard (version 2.25.1), a step through which, all the reads of a single file are assigned into one read group. Sorting and indexing of this file, which is necessary for subsequent steps could also be integrated into the same command.

Owing to the systemic technical errors of NGS data processing, base quality score alone may not be a proper indication of true base call errors. To address this issue GATK has introduced base quality score recalibration (BQSR). According to the official website available at GATK1, BQSR is the machine learning algorithm introduced by GATK that enables improved overall base qualities, that subsequently increases the variant call accuracy. With the latest version of GATK,, the process involves two major steps. Initially, a model of covariation along with a recalibration table is produced on the BAM input from the previous step, with the BaseRecalibrator tool, based on an indexed VCF file of known variants and SNP’s downloaded from dbSNP for the respective reference sequence and various covariates including read group, machine cycle number, reported quality score, and nucleotide context. Secondly, using the ApplyBQSR tool, a new BAM output is produced with adjusted base quality scores, depending on the built model. Additionally, the effects of recalibration are assessed by building another model for the new BAM output with the BaseRecalibrator tool, and plots are generated with the AnalyzeCovariates tool to compare the effects of the process. It is noteworthy that the AnalyzeCovariates tool requires other tools installed like R libraries, ggplot2, gsalib, and reshape to function.

Variant calling and filtering

Variant calling of Human mitochondrial genome is possible through the mitochondrial mode of GATK (version Mutect2 (Benjamin et al., 2019). Through mitochondrial mode, it allows sensitive calling of short nucleotide variants and indels at high depths with local assembly of haplotypes. The output is a raw highly sensitive VCF call set. Due to various types of errors and biases in the data, it demand the generation of a high-quality set of variants. To identify false positives out of the original VCF files and acquire a balance between sensitivity and specificity, necessary filters should be applied through variant filtering. GATK (version offers several filtering tools based on different strategies used (Pfifer, 2017; Van der Auwera et al., 2013). FilterMutectCalls is the recommended tool for this scenario (Benjamin et al., 2019) through which possible false-positive artifacts will be flagged in the output VCF by its ‘failed filter’ while the remaining would be marked as ‘PASS’ (Van der Auwera et al., 2013; Roy et al. 2018). With the SelectVariants tool, they can then be excluded from the final VCF output file.

Generating coverage plots and VCF file report

With SAMtools (version 1.9), coverage plots can be created for the final BAM output of GATK (version Additionally, with the DISCVRSeq (version1.21) tool, a VCF file report can be generated using a previously compressed and indexed final VCF file.

Determining heteroplasmy levels, contamination, and haplogroup detection

High throughput sequencing has enabled the detection of heteroplasmy levels that are below 10%, which was not possible with previous sequencing methods (Mertens et al., 2019). mtDNA-Server (Weissensteiner et al., 2016), a free online data analysis server for mtDNA, reliably detects levels of heteroplasmy in NGS data 1% or above. The standalone version of mtDNA-Server, which can be locally installed, Mutserve (version 2.0.0-rc7) was used to detect the level of heteroplasmy in this pipeline and provided a sorted and indexed BAM as input.

Sample cross-contamination during next generation sequencing of mtDNA proves to be challenging at the data analysis phase as they may present themselves as low-level heteroplasmy (Dickins et al., 2014; Li et al., 2010). Haplocheck is a software tool developed to estimate the contamination level of mtDNA samples through mitochondrial phylogeny (Weissensteiner et al.,2021). It can be used as a cloud service or be locally installed. Locally installed Haplocheck (version 1.3.2), was used in analyzing NGS data for contamination.

Distinct regions of the mtDNA genome sequence that group together, reflecting phylogenetic origin through different maternal lineages are defined as mitochondrial haplotypes. These haplotypes can be assigned to haplogroups that represent the main branching points of the mitochondrial phylogenetic tree as they show how specific SNPs or variations have been accumulated through a certain matrilineage (Pipek et al., 2019; Samuels et al., 2006). Determining haplogroup in mitochondrial DNA sequence studies is important both to trace these lineages in human population genetics and to identify their various associations with diseases and health conditions. Haplogrep 2 (Weissenteiner et al., 2016) is a popular tool used to classify haplogroups in NGS studies. Local installation of Haplogrep 2 (version 2.1.25) was used to identify haplogroups of preferred VCF input files.


Variant Annotation and visualisation

Assigning related biological information to identified variants is defined as variant annotation. There are several computational tools for human mitochondrial DNA analysis. Query with these tools provide sequencing data against variant databases and designate a set of associated metadata including the location compared to the reference sequence, respective change in amino acid and cDNA sequence, prediction of functional effects, and their presence in various databases (Roy et al., 2018; Wadapurkar and Vyas, 2018). Variant Effect Predictor (VEP) (McLaren et al., 2016) by ENSEMBLE project is a tool available at http://www.ensembl.org/ that accepts the final VCF file as input and enables the download of the annotated file in several formats. Via integrating SIFT (Kumar et al., 2009) and Polyphen (Adzhubei et al., 2010) it allows prediction of functional effect, as well as the discovery of genomic location, substitution effect of amino acid, and codon change. A txt format output, downloaded from VEP website, following annotation of the final VCF generated with the current pipeline is given in Supplementary file 52.

The final step of NGS variant calling pipelines is the visualisation of these data using genome browsers and visualisation tools. This task was performed with Integrative Genomics Viewer (IGV version 2.9.2) (Robinson et al., 2011; Thorvaldsottir et al., 2013) provided by Broad Institute of Harvard and MIT. It is a user-friendly and high performing interactive tool for exploring NGS data. By enabling read alignment examination, this step allowed further confirmation of called variant through visual estimation of it being true or a sequencing artifact. Additionally, through this step, more associated information of variants like mapping quality and variant impact acquired could be viewed individually (Figure 1).


Figure 1. An A>G base substitution at position 8860 of human mitochondrial genome, aligned with rCRS Human Mitochondrial Genome Reference sequence zoomed for 12 base pairs length in IGV 2.9.2.



Limitations and perspective

Initially, it is important to notice that the sensitivity of heteroplasmy level detection correlates with increasing coverage depths (Holland et al., 2011; Zhang et al., 2012). At the same time, data generated with higher depths of coverage requires significant computer storage and advanced computers for data handling without compromising efficiency. Secondly, a signal from a very low-frequency variant is not discernable from that of a sequencing error. Finding the right balance between precision and sensitivity during data analysis, holds key to identify these variants. As desired, during variant filtering with FilterMutectCalls, the level for -f-score-beta argument could be adjusted between precision and recall, whereas 1 is the default value, 0.5 indicates higher precision over recall, and 2 indicates the higher recall over precision. However, other than bioinformatic analysis, criteria for quality control are also a limiting factor for detecting levels of heteroplasmies. It has been found that optimal conditions for primary PCR amplification and library preparation for high throughput sequencing are critically important as substandard conditions result in inflated variant frequencies (Mertens et al.,2019). Evidently, maximum accuracy in variant calling through NGS data demands high proficiency from laboratory practices to computational analysis. Nevertheless, despite the challenges present in the field of mitochondrial high throughput sequencing data processing, with rapidly improving and newly developing analysis tools coupled with other usual benefits offered via all massive parallel sequencing methods, NGS is likely to become predominant over previous sequencing methods in the foreseeable future.


This work was supported by National Research Council, Sri Lanka Grant No: 17-020 and constituted part of PhD studies of Jayasekera BMLP.

Key Points

Targeted Sequencing of Human mitochondrial genome

Bioinformatics pipeline for variant detection

Next Generation Sequence data analysis of mtDNA



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