Get full sequence from sorted bam file

Question

[wang.yiguan]

Hi, I got an indexed and sorted bam file from a colleague, and I also have the reference genome. My question is: how can I get a full sequence (eg. fasta file) from the bam file?

I googled some tools, but most of them are used to convert bam file into fasta, and the fasta file still contains segments of reads. I do not want to have these reads, I want to have a whole sequence.

Appreciated it for your answers!

Answer 1

[GenoMax]

You can create a consensus sequence from an aligned BAM file after calling SNP's. Basic procedure is described in this bcftools consensus help page.

[wang.yiguan]

Thank you very much! Your suggestion works good for me!