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 Variant Callers

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

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.

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
QIAGEN CLC Genomics Workbench	N/A		SmallVariant
CNVKit	N/A		CNVReadDepth
CNVReporter	0.01		CNVReadDepth
CnvXhmm	1.0		CNVReadDepth
CNVnator	N/A		CNVReadDepth
CytoScanHDArray	Multi-Sample Viewer:1.0.0.71		Unknown
DeepVariant	1.0.0		SmallVariant
Dragen Array Cyto	1.2.0, 1.1.0, 1.0.0	V37.0 and up	Array
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
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		SVSplitEnd
Sophia	0.0.2		SmallVariant
SophiaCnv	2.0.1		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.