Mitochondrial Calling

Typically, there are approximately 100 mitochondria in each mammalian cell, and 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 now processes chrM through a continuous AF pipeline. In this case, a single ALT allele is considered, and the AF is estimated, and can be anywhere between 0% and 100%.

QUAL is not output in the chrM variant records. Instead, the confidence score is INFO/LOD

##INFO=<ID=LOD,Number=1,Type=Float,Description="Variant LOD score">

which gives the confidence that a variant is present at a given locus.

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, and if INFO/LOD > vc-lod-call-threshold (default = 4), then the FORMAT/GT is hard-coded to 0/1, and the FORMAT/AF yields an estimate on the variant allele frequency, which ranges anywhere within [0,1].

The following filters can be applied to mitochondrial variant calls.

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--vc-lod-call-threshold

LOD threshold for emitting calls in the VCF. The default is 4.

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--vc-lod-filter-threshold

LOD threshold to mark emitted VCF calls as filtered. The default is 6.3.

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If INFO/LOD < vc-lod-call-threshold, the variant is not emitted in the VCF.

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If INFO/LOD > vc-lod-call-threshold but INFO/LOD < vc-lod-filter-threshold the variant is emitted in the VCF but FILTER=lod_fstar.

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If INFO/LOD > vc-lod-call-threshold and INFO/LOD > vc-lod-filter-threshold, the variant is emitted in the VCF and FILTER=PASS.

The following are example VCF records on the chrM, showing one call with very high AF and another with very low AF. In both cases FORMAT/LOD > emit_threshold. FORMAT/LOD is also > lod_fstar threshold, so the FILTER annotation is PASS.

chrM 2259 . C T . PASS DP=9791;MQ=60.00;LOD=38838.40;FractionInformativeReads=0.994 GT:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:5,9729:0.999:1,5007:4,4722:9734:3,2,4885,4844:1,4,4807,4922

chrM 16192 . C T . PASS DP=9644;MQ=60.00;LOD=26.12;FractionInformativeReads=0.992 GT:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:9537,26:0.003:5530,16:4007,10:9563:4484,5053,13,13:4961,4576,19,