Difference between vcf2fq and bcftools consensus
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
• 32 views
Read more here: Source link