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 |
|---|---|---|
V36.0 | SNV, CNV, STR, SV, Targeted, MRJD, JSON PGx* | |
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 |
5.12, 5.20 | SmallVariant | ||
N/A | SmallVariant | ||
1.38 | CNVReadDepth | ||
N/A | SmallVariant | ||
N/A | CNVReadDepth | ||
CNVReporter | 0.01 | CNVReadDepth | |
1.0 | CNVReadDepth | ||
N/A | CNVReadDepth | ||
Multi-Sample Viewer:1.0.0.71 | Unknown | ||
1.0.0 | SmallVariant | ||
1.2.0, 1.1.0, 1.0.0 | V37.0 and up | Array | |
N/A | SVSplitEnd | ||
0.1 | CNVReadDepth | ||
ExomeDepthAM | 0.1 | Private fork of ExomeDepth | CNVReadDepth |
N/A | SmallVariant | ||
3, 3.4, 3.5, 2014, 4, 4.1 | SmallVariant | ||
GATK Mutect | N/A | SmallVariant | |
Scramble | Running: scramble2vcf.pl | SmallVariant | |
1.4 | SmallVariant | ||
4.x, 5.x and not: 5.12, 5.20 | SmallVariant | ||
2.2.0 | SVSplitEnd | ||
N/A | SmallVariant | ||
2.X | SmallVariant | ||
2.1.1 | SVSplitEnd | ||
2.2.4 | SmallVariant | ||
2.2.4 | SVSplitEnd | ||
2.X | SVSplitEnd | ||
5.2.9 | SmallVariant | ||
201808, 201911, 202010 | SmallVariant | ||
201808.03 | SmallVariant | ||
2.0.6 | SVSplitEnd | ||
0.0.2 | SmallVariant | ||
2.0.1 | CNVReadDepth | ||
2.4.5 | SmallVariant | ||
N/A | SmallVariant | ||
N/A | SVSplitEnd |
Internally the list is also called a list of Emedgenizer / Emedgenizers. Emedgenizer means to normalize a VCF to an expected format for the system.
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