Entering edit mode
6.4 years ago
eric_fournier8
•
0
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
