bcftools consensus warning
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Entering edit mode
4 months ago

Hi,

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?

Thanks!

bcftools consensus pipeline • 128 views
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