fasta sequence does not match the REF allele (again)

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Assessment

Difficulty
5/5
Estimated time
Over a week
Newbie friendliness
15/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Domain
bioinformatics

Research direction

Start by reviewing the reported bcftools consensus error at NC_024336.1:15480326 and the prior troubleshooting references to norm and filter. The issue does not name source files or tests; done would require determining why the reported FASTA base and REF allele disagree and documenting or reproducing a concrete fix.

Written by the indexing model from the issue text.

Description

enhancement

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

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