Variant calling with Freebayes gives M as a reference nucleotide call

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?

variant snp next-gen-sequencing freebayes

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updated 4.5 years ago by Ram

• written 11.8 years ago by stefano.iantorno •

1 answer

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)

• 0 views • link

updated 4.5 years ago by Ram

• written 11.8 years ago by mbio.kyle

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

• 0 views • link

updated 4.5 years ago by Ram

• written 11.8 years ago by stefano.iantorno •