Variant calling with Freebayes gives M as a reference nucleotide call

Question

[stefano.iantorno]

Hello,

I've used Freebayes to call variants on 12 samples. However when I inspect the variant calls, I have a handful of positions in which the REF allele contains nucleotide calls that are not A, G, C, T or N.

For instance:

LmjF.06 2454    .       AM      AA,AC,GC
LmjF.06 81319   .       CGAM    CGAA,CGAC,TGAC

Any idea what's going on, and how to fix it?

Answer 1

[mbio.kyle]

First time answering here so excuse any mistakes!

But I believe that the M comes from the extended Nucleic Acid notation.

M = A C (amino)

Here is the rest (from wikipedia)

• R = G A (purine)
• Y = T C (pyrimidine)
• K = G T (keto)
• S = G C (strong bonds)
• W = A T (weak bonds)
• B = G T C (all but A)
• D = G A T (all but C)
• H = A C T (all but G)
• V = G C A (all but T)
• N = A G C T (any)

[stefano.iantorno]

Thank you! Is there a way to run freebayes so that it won't call any ambiguous bases?