I am trying to generate a consensus using an assembly that I built myself. But I get the following warning:
Warning: Sequence "LT578325.1" not in reads.vcf.gz
I used the command:
bcftools consensus -I -f reference.fasta reads.vcf.gz > consensus.fa
The VCF was generated using samtools mpileup | bcftoools call.
A similar discussion from some 3 years ago (Warning while finding bcftools consensus) seems to suggest it could be a header problem... any idea?