I am working in Genome assembly(Reference Guided), I want to create consensus sequence from bam file.I tried bcftools and vcf-consensus. But, I got some IUPAC code. I want consensus sequence without IUPAC Code.
I want to create like this:
Please suggest any tool or software. Thanks in advance.
Can't you write a bit of code to "resolve" these ambiguous nucleotides, and randomly chose one of the options? It's obviously not fully correct, but what do you think is the best for a heterozygous variant?
Did you find out how to create the consensus sequences without IUPAC codes? I'm having the same problem using samtools and bcftools.