Difference between genotype 0/1, 1/0, 0/2, 2/0?

Question

[nsmi8446]

Hi all,

Apologies if this has already been answered before. I couldn't find an answer on here.

I'm wondering what the difference is between genotypes 0/1, 1/0, 0/2, 2/0 in a vcf file? I assume there isn't one.

I've taken a look at this page without luck: https://samtools.github.io/hts-specs/VCFv4.1.pdf

Thanks in advance.

Answer 1

[gayachit]

You need to read the manual carefully. Its there on page 5 under genotype fields.

[Kevin Blighe]

Indeed, you will see a '2' in the GT field of a VCF record if it is a multi-allelic site:

• 0 = ref base
• 1 = first alternate base
• 2 = second alternate base

Many programs cannot support multi-allelic records, so, you can split these into 2 (or more) records via:

bcftools norm -m-any