Consensus sequence from vcf file

Question

I am generating a consensus sequence for SARS-Cov-2. I am visually inspecting every candidate SNP in a pileup.

Sometimes I find that there are two consistent variants for the same position, but I can only generate one consensus sequence.

Which variant should I target:

• The majority variant
• The minoritarian one if I find that this SNP is under-reported in other public samples?
• Are both required

What one is best practice?

Answer 1

Making a consensus sequence tends to involve some arbitrary decisions. In this case, the common practices are:

1. Use the ancestral allele (this isn't always apparent)
2. Use the most common allele
3. Randomly choose

I think 1 and 2 are generally preferred, with 2 being easier to implement.