Mitochondrial Calling

Typically, there are approximately 100 mitochondria in each mammalian cell. Each mitochondrion harbors 2–10 copies of mitochondrial DNA (mtDNA). For example, if 20% of the chrM copies have a variant, then the allele frequency (AF) is 20%. This is also referred to as continuous allele frequency. The expectation is that the AF of variants on chrM is anywhere between 0% and 100%.

DRAGEN processes chrM through a continuous AF pipeline, which is similar to the somatic variant calling pipeline. In this case, a single ALT allele is considered and the AF is estimated. The estimated AF can be anywhere between 0% and 100%.

QUAL is not output in the chrM variant records. Instead, the confidence score is FORMAT/SQ, which gives the Phred-scaled confidence that a variant is present at a given locus.

##FORMAT=<ID=SQ,Number=A,Type=Float,Description="Somatic quality">

GQ is not output in the chrM variant records because DRAGEN doesn't test for multiple diploid genotype candidates. Instead, an ALT allele is considered as a candidate variant. If FORMAT/SQ> vc-sq-call-threshold (default = 3.0), then the FORMAT/GT is set to 0/1. The FORMAT/AF yields an estimate on the variant allele frequency, which ranges anywhere within [0,1]. For very high allele frequencies (AF ≥ 95%) the FORMAT/GT is set to 1/1.

You can apply the following filters to mitochondrial variant calls.

--vc-sq-call-threshold

Set the SQ threshold for emitting calls in the VCF. The default is 0.1.

--vc-sq-filter-threshold

Set the SQ threshold to mark emitted VCF calls as filtered. The default is 3.0.

--vc-enable-triallelic-filter

Enable the multiallelic filter. The default value is false.

If FORMAT/SQ < vc-sq-call-threshold, the variant is not output in the VCF.
If FORMAT/SQ > vc-sq-call-threshold but FORMAT/SQ < vc-sq-filter-threshold the variant is output in the VCF but FILTER=weak_evidence.
If FORMAT/SQ> vc-sq-call-threshold, FORMAT/SQ > vc-sq-filter-threshold, and no other filters are triggered, the variant is output in the VCF and FILTER=PASS.

The following are example VCF records on the chrM. The examples shows one call with very high AF and another with very low AF. In both cases FORMAT/SQ > vc-sq-call-threshold. FORMAT/SQ is also > vc-sq-filter-threshold, so the FILTER annotation is PASS.

chrM 513 . GCA G . PASS DP=4937;MQ=235.28;FractionInformativeReads=0.883

GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 1/1:95.46:33,4327:0.992:7,1081:26,3246:4360:31,2,2371,1956:10,23,2811,1516

chrM 1713 . A G . PASS DP=7175;MQ=165.91;FractionInformativeReads=0.995

GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.49:7122,20:0.003:3066,10:4056,10:7142:3896,3226,8,12:3605,3517,10,10