Two adjacent SNPs reported rather then a MNP?

[Jesspalmer92]

Hello,

Apologies, I wanted to write this on the mailing list but there is a 'Banned content warning' on the google group and it cannot be accessed.

I have an output of the following:

Most of the time, I have noticed if there are adjacent SNPs, the tool will output as a MNP but occasionally, as in the example above, they are separate.

The true mutation, checked in IGV is pos 378 : AT > GT, AC.

This is messing up my downstream analysis in my pipeline as when output as in the image, my tool is predicting there might be the presence of GC in one of the codons.

I have three questions about this:

1. Is this a bug, would you have expected the Freebayes output for this mutation to be displayed as a MNP instead as it involves adjacent positions?
2. If not a bug, do you know why some mutations are displayed as MNPs and some are multiple SNPs in close proximity to one another?
3. I can't find this information anywhere so could you please confirm, if a SNP is output, can I assume the (at least) 2 leading and 2 trailing nucleotides to the SNP are wildtype? This is important as I can fix my pipeline if at least this can be confirmed.

Thank you in advance!