How to get consensus sequences in FASTA format from BAM

Question

[phongphak.06]

I've searched for an answer but I only got this command:

samtools mpileup -uf reference.fa aligment.bam | bcftools view -cg - |
vcfutils.pl vcf2fq

Anyway, I cannot use it to generate consensus sequences since the changing of the version of each tool, which mean the options are also changed.

Is there any idea that can to this?

[finswimmer]

• http://www.htslib.org/doc/bcftools.html#consensus
• https://samtools.github.io/bcftools/howtos/consensus-sequence.html

[phongphak.06]

Thank you so much for your help.

So I'll try this :)