Difference between vcf2fq and bcftools consensus

Question

[antoine.fauchois92]

Hi everybody,

I'm working for generate consensus sequence and I'm interogating myself about the differences of work process between bcftools consensus and vcf2fq from vcfutils.pl. In the one hand, thanks to vcf2fq, I can generate consensus sequence with the following command:

bcftools mpileup -f {ref_seq} {input_file.bam} | \
bcftools call -c | \
bcftools annotate --rename-chrs {rename_file} | \
vcfutils.pl vcf2fq > {output_file.fastq}")

In the other and, it can be perform with bcftools consensus with the following commands:

bcftools mpileup -Ou -f {ref_seq.fasta} {input.bam} | bcftools call -mv -Oz --threads 10 -o {output.vcf.gz}
bcftools index {input.vcf.gz}
bcftools consensus -f {ref_seq.fasta} {input.vcf.gz}

Is there a difference ? Is there a better one than other ? Or is there a recommanded tool for a specific case ?

Best regards, Antoine

Answer 1

[Istvan Albert]

The tools do change - especially when it comes to reconciling close variants.

But asking is it better or worse does not have an easy answer since the changes are not all that well documents.

All of us are, of course, are hoping that newer versions are better, but whether that is better for the author or all of us ... is less clear.