Bcftools consensus error

Hi all-

First of all- thanks for setting up this discussion board, it is incredibly helpful.

We have been using the ARTIC lib prep and bioinformatics protocol for all of our SARS-nCoV-2 sequencing and it has worked great. When running the most recent version of the bioinformatic pipeline (using nanopolish), I have had two samples end in a variation of the following error:

command failed: bcftools consensus

The fasta sequence does not match the REF allele at MN908947.3:11916:
.vcf: [C]
.vcf: [T] <- (ALT)
.fa: [N]

In this example, I went through and looked at the called variants listed in the various VCF file, and a C to T SNP at position 11916 is listed in the samplename.fail.vcf, samplename.pass.vcf, and samplename.merge.vcf files. I can fix this error by manually masking the site in samplename.coverage_mask.txt file and redoing the consensus generation step and the position is masked with an N. Although it does look like there is a genuine SNP at this position.

As anyone else seen this problem? Is there a potential workaround? Any advice here would be greatly appreciated. Please let me know if more info is needed to troubleshoot.


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Thanks for this report: it was actually fixed in the past few days, more details here:

You can update easily by running:

pip install --force-reinstall git+https://github.com/artic-network/fieldbioinformatics.git

And it will be baked into a new release candidate (1.1.0-rc2) in next day or two.

Thanks, Nick! Sorry for not checking the github repo first.

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