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: [T] <- (ALT)
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.