> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/tertiary-analysis-pipeline/how-does-emedgene-analyze-merge-variants-from-different-sources.md).

# Integrating variant annotations from multiple sources

The Emedgene pipeline prioritizes variant annotations based on the calling methodology rank order. The first appearance of a variant is annotated according to the following hierarchy:

1. TARGETED
2. STAR\_ALLELE
3. STR\_REPEAT\_EXPANSION
4. MRJD
5. FORCED\_GENOTYPING
6. SMALL\_VARIANT
7. CNV\_READ\_DEPTH
8. SV\_SPLIT\_END
9. UNKNOWN

#### Identical Variant Criteria

Variants are considered identical if they share the same:

* Chromosome
* Position
* Reference allele (REF)
* Alternate allele (ALT)

#### Limitation

When applied to Copy Number Variants (CNVs), this approach may merge variants even if they have different lengths.


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