Hello everyone, I try to use the bcftools consensus command, but it seems something is missing. I have designed my commands on the two sources below, and the manual.
The first command tried:
bcftools consensus -s sample.vcf.gz -f reference.fa > output.fa
cat reference.fa | bcftools consensus -s sample.vcf.gz > output.fa
But it does not seem to work in both cases. Would anyone have an idea of what could be wrong here?