Getting a consensus sequence with bcftools

Question

[owenz]

I am trying to update a script for using on Hep C viral data. I have used bwa and samtools to align to reference and create a VCF file with mpileup.

What I am trying to do is to create a consensus FASTA sequence file with bcftools consensus command. This does not work.

bcftools consensus -f HCV1.fasta all_snps.vcf.gz >consensus.fa

I am not sure what to input as part of the -s flag. I am not sure I am understanding the biology behind it.

Thanks

[GenoMax]

This does not work.

What happens? You don't get a consensus?

[owenz]

I get the following msg

Note: the --sample option not given, applying all records

I am not sure what to add as part of the --sample flag

[GenoMax]

If you file has a single sample then that is just an informational message.

[owenz]

The original script was written to take more than one file. BUt I guess I should create a new script for the consensus part to take up one file only?

The consensus file is being created but it is empty

[GenoMax]

If the file is empty then that is a different problem. Are the chromosome names matching in your VCF and the reference?

VCF's can have more than one sample (when the -s option would become relevant) so it is not about script per se.

[owenz]

Yes the VCF and the reference fasta have matching chromosome names

[WouterDeCoster]

Hi owenz,

There is no need to delete threads.
Thank you,

Wouter

[owenz]

Hi Wouter,

Thanks for letting me know. I am new here.

Owen