Call and Compare SNPs in Geneious Prime

This series shows how to call and compare single nucleotide polymorphisms on an already-mapped NGS contig in Geneious Prime. Use Find Variations/SNPs to call SNPs and filter sequencing errors, then use Compare Annotations to exclude SNPs that overlap low-coverage regions or set a minimum coverage threshold directly in the SNP finder. The series spans two videos, 2 minutes each.

Course Content

Calling SNPs

Call SNPs on a mapped contig using Find Variations/SNPs, setting the genetic code to match your sample so Geneious can flag amino acid changes. Review SNP details by hovering in the Variance track, or export the Polymorphism annotations as a CSV table.
LENGTH 2 minutes

Comparing SNPs

Compare a Polymorphism track against a Low Coverage track using Compare Annotations, selecting A-B results to exclude SNPs that fall in low-coverage regions. Or set a minimum coverage value directly in Find Variations/SNPs to filter automatically.
LENGTH 2 minutes

Recommended Resources

Can I call SNPs on individual sequences aligned to a reference?

How to call SNPs on different assmeblies and alignments.

Manual for Finding Variations/SNPs

A guide to using the Find Variations/SNPs feature in Geneious.

Plugin - BBDuk Trimmer

Download the plugin for quality trimming and filtering your sequences.

Which map to reference assembly algorithm is best for my data?

Advantages and disadvantages of different map to reference algorithms.

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