Difference between vcf2fq and bcftools consensus

Difference between vcf2fq and bcftools consensus

1

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


bcftools

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