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.