Supported variant callers

Emedgene provides the tightest integration with DRAGEN for germline variation analysis, providing accuracy, comprehensiveness, and efficiency, spanning variant calling through interpretation and report generation.

Compatibility with DRAGEN and DRAGEN Array Variant Callers

DRAGEN	Emedgene	Available Callers
4.3 See full compatibility table	V36.0	SNV, CNV, STR, SV (del/dup/ins), Targeted, MRJD, JSON PGx*
4.2 See full compatibility table	V35.0	SNV, CNV, STR, SV (del/dup/ins), SMN, JSON PGx*
4.2	Recommended: V34.0	SNV, CNV, STR, SV (del/dup/ins), SMN
4.0	Recommended: V34.0	SNV, CNV, STR, SV (del/dup/ins)
3.10	Recommended: V34.0	SNV, CNV, STR, SV (del/dup/ins)
3.6-3.9	Recommended: V34.0	SNV

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DRAGEN Array	Emedgene	Available Callers
1.2	V37.0	Cyto

MRJD caller

MRJD is a haplotype-based de novo small variant caller designed to work in segmental duplication regions (which make up ~5% of the genome and are hard to map accurately).

It detects variants in paralogous regions by gathering reads that might be mapped to similar genomic regions. This enables de novo germline small variant calling even in areas where standard callers struggle.

Genes covered by MRJD:

Gene	Condition	Application
PMS2	Lynch Syndrome	Pharmacogenomics
SMN1 (small)	Spinal Muscular Atrophy	Carrier Screening
STRC	Nonsyndromic Hearing Loss	Carrier Screening
NEB	Nemaline Myopathy	Carrier Screening
TTN	Cardiomyopathy	ACMG Secondary, Newborn Screen
IKBKG	Incontinentia Pigmenti / Hypohidrotic Ectodermal Dysplasia	Newborn Screening

Important: When running DRAGEN through Emedgene, MRJD high sensitivity mode is enabled by default.

Expanded targeted caller support

Targeted caller support has expanded to cover GBA, HBA, and CYP21A2, in addition to previously supported targets.

Just like MRJD, some targeted caller outputs may also be ambiguously placed and linked with JIDS. These will:

• Be displayed with an "Ambiguous calling" tag.

• Be filterable using the Calling Methodology filter.

Genes covered by targeted caller expansion:

Gene	Condition	Application
CYP2D6	NA	Pharmacogenomics
SMN1	Spinal Muscular Atrophy	Carrier Screening
GBA	Gaucher’s Disease	Carrier Screening
CYP2B6	NA	Pharmacogenomics
HBA1/2	Alpha-thalassemia	Carrier Screening
CYP21A2	Congenital Adrenal Hyperplasia	Carrier Screening
RHD/RHCE	RH Blood Type	Blood Typing
LPA	Cardiac Disease Risk	Cardiovascular Disease

Extensive Compatibility with Additional Variant Callers

The Emedgene platform supports a variety of variant callers and applies specific quality parameters for each. The quality assessment is an essential step in the Emedgene pipeline because variants with low quality will not be considered by the AI components.

If the variant caller is not supported or not recognized, a default quality function will be applied. The default parameters are built on GT (genotype), depth (DP) and allele bias (AB). These fields are mandatory, and their absence will induce “Low quality” for all variants.

The following variant callers are currently supported on the Emedgene pipeline, providing a header with the variant caller command line should be present within the VCF headers.

Additional callers can be supported on demand under licence.

Var caller / VCF	Supported versions	Notes	Calling Methodology
AED CNV	N/A	Affymetrix Extensible Data. converted to VCF	CNVReadDepth
ION AMPLISEQ	5.12, 5.20		SmallVariant
Atlas-SNP2	N/A		SmallVariant
CanvasCNV	1.38		CNVReadDepth
Clair3		V37 & up	SmallVariant
QIAGEN CLC Genomics Workbench	N/A		SmallVariant
ClinSV	N/A		SVSplitEnd
CNVKit	N/A		CNVReadDepth
CNVReporter	0.01		CNVReadDepth
CnvXhmm	1.0		CNVReadDepth
CNVnator	N/A		CNVReadDepth
cuteSV	2.02	V37 & up	SVSplitEnd
CytoScanHDArray	Multi-Sample Viewer:1.0.0.71		Unknown
DeepVariant	1.0.0		SmallVariant
eKLIPse	N/A		SVSplitEnd
ExomeDepth	0.1		CNVReadDepth
ExomeDepthAM	0.1	Private fork of ExomeDepth	CNVReadDepth
Freebayes	N/A		SmallVariant
GATK	3, 3.4, 3.5, 2014, 4, 4.1		SmallVariant
GATK Mutect	N/A		SmallVariant
GATKScramble	Scramble	Running: scramble2vcf.pl	SmallVariant
GLNEXUSSNV	1.4		SmallVariant
IONTorrent	4.x, 5.x and not: 5.12, 5.20		SmallVariant
IONTorrent CNV	5.16		CNVReadDepth
MELT	2.2.0		SVSplitEnd
Mity	N/A		SmallVariant
NextGene	2.X		SmallVariant
cuteSV for ONT	2.1.1		SVSplitEnd
PAV	2.2.4		SmallVariant
PAVSV	2.2.4		SVSplitEnd
PBSV	2.X		SVSplitEnd
Pisces	5.2.9		SmallVariant
Sentieon	201808, 201911, 202010		SmallVariant
SentieonDNAScope	201808.03		SmallVariant
Sniffles	2.0.6, 2.0.7, 2.5		SVSplitEnd
Sophia	0.0.2		SmallVariant
SophiaCnv	2.0.1		CNVReadDepth
Spectre		V37 & up	CNVReadDepth
Starling	2.4.5		SmallVariant
Strelka	N/A		SmallVariant
Witty	N/A		SVSplitEnd

Internally the list is also called a list of Emedgenizer / Emedgenizers. &#xNAN;Emedgenizer means to normalize a VCF to an expected format for the system.