BAM/SAM to aligned FASTA file

Question

[ryan.englander]

Hi,

I have a reference genome and reads from a cancer cell line aligned to that reference in a BAM and SAM file. I need to convert the BAM file into a FASTA file where the cancer consensus sequence is aligned to the reference genome so I can identify . Other threads on BioStars addressing this question explain how to generate FASTQ and FASTA files based off the BAM file, but don't explain how to align those sequences to the reference. Thanks so much in advance!

Answer 1

[Tonor]

To align your consensus sequence to your reference sequence you will need to use an alignment tool to create a multiple sequence alignment, such as:

MAFFT, MEGA, CLUSTAL, and loads of others

These tools don't care that one is a consensus, and one is reference, it just aligns all the sequences you give it together