fasta sequence does not match the REF allele (again)

[LennWhy]

Hi,

I have been trying to generate a consensus sequence using bcftools consensus, but keep failing miserably. The error that i keep getting is:

The fasta sequence does not match the REF allele at NC_024336.1:15480326: .vcf: [N] .vcf: [G] <- (ALT) .fa: [R]ACAAAAGGA

I noticed that this error has occurred for many, and have read how it was troubleshot using 'norm' and 'filter' in previous issues; however even after all this, I still encounter the same issues. The reference genome that I use for normalising my indels and building the consensus sequence is the same, and so I am not sure what is happening.

Can anyone please advise?

Many thanks! Lenny

[pd3]

The program suggests that your reference sequence contains iupac ambiguity codes ("R"), which are not supported by VCF and bcftools.