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- 2 years, 3 months ago
Posts by donutbrew
... AFAIK, you can't use a modified reference genome with bcftools consensus. You'll get an error like "The fasta sequence does not match the REF allele at..." and the consensus output will die at that point (where the 'N' is in the reference). I You CAN, however, generate the pileup with the masked re ...
... I'm also having this issue. There doesn't seem to be any prebaked solution to converting an mpileup to a consensus sequence that will include both SNPs and INDELs. Even when I can see the deletion in the alignment in igv, and the pileup recognizes it, the resulting vcf going through bcftools gets ri ...
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