# Tertiary analysis pipeline

- [Supported reference genome assemblies](https://help.emg.illumina.com/emedgene-analyze-manual/tertiary-analysis-pipeline/which_reference_genomes_can_i_use.md)
- [Joint calling in Emedgene](https://help.emg.illumina.com/emedgene-analyze-manual/tertiary-analysis-pipeline/how_does_joint_calling_work_on_emedgene.md)
- [Transcript prioritization logic](https://help.emg.illumina.com/emedgene-analyze-manual/tertiary-analysis-pipeline/how_does_emedgene_analyze_prioritize_transcripts.md)
- [Emedgene annotations and update frequency](https://help.emg.illumina.com/emedgene-analyze-manual/tertiary-analysis-pipeline/annotation_updates.md)
- [Variant effect and severity calculation](https://help.emg.illumina.com/emedgene-analyze-manual/tertiary-analysis-pipeline/how_does_emedgene_calculate_variant_effect_and_severity.md)
- [Integrating variant annotations from multiple sources](https://help.emg.illumina.com/emedgene-analyze-manual/tertiary-analysis-pipeline/how-does-emedgene-analyze-merge-variants-from-different-sources.md)
- [Processing multi-nucleotide variants](https://help.emg.illumina.com/emedgene-analyze-manual/tertiary-analysis-pipeline/how_are_mnvs_handled_on_the_platform.md)
- [Annotations from organization databases](https://help.emg.illumina.com/emedgene-analyze-manual/tertiary-analysis-pipeline/annotations-from-organization-databases.md)