Hi everyone,

i used smalt to map reads against a virus reference genome. To obtain the consensus sequence i have executed a command similar to this one;

samtools mpileup -uf database.fasta aln.sorted.bam | bcftools view -cg - | vcfutils.pl

In the final consensus sequence i have some ambiguous bases. Now, i am wondering what is the default allele frequency value (50% ?, 30% ?, ?) to call ambiguity. I didn't find any help in the samtools and bcftools documentation.

Thank you in advance for your help.

Eric