Emedgene provides the tightest integration with DRAGEN for germline variation analysis, providing accuracy, comprehensiveness, and efficiency, spanning variant calling through interpretation and report generation.
100.40.0+
SNV, CNV, STR, SV (del/dup/ins), Targeted, MRJD, Ploidy TruPath: SNV, SV, MRJD
4.2
All
SNV, CNV, STR, SV (del/dup/ins), SMN
4.0
All
SNV, CNV, STR, SV (del/dup/ins)
3.10
All
SNV, CNV, STR, SV (del/dup/ins)
3.6-3.9
All
SNV
1.4
100.40.0+
Cyto
1.3
100.39.0+
Cyto
1.2
37.0+
Cyto
*to modify the case pipeline version refer to Pipeline versions.
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.
Internally, this list is referred to as the Emedgenizers list. An Emedgenizer is a tool that normalizes VCF files to the system’s expected format for each variant caller.
Additional callers can be supported on demand under license.
Clair3
v37.0+
SmallVariant
ClinSV
N/A
SVSplitEnd
CNVReporter
0.01
CNVReadDepth
cuteSV
2.02
v37.0+
SVSplitEnd
ExomeDepthAM
0.1
Private fork of ExomeDepth
CNVReadDepth
Spectre
v37.0+
CNVReadDepth
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