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.