Extract alignment in fasta format from BAM/SAM file

Question

[SaltedPork]

Hi, I have a BAM file from aligning reads to a reference. What I would like is a fasta alignment file for each read showing the alignment between read and reference ie.

>read1

------A--C------GTATCTAGTCATGACT----------

Is there a tool/method that I can use that can extract the alignmments from a BAM and show in fasta format.

[cmdcolin]

looks x-post on reddit https://www.reddit.com/r/bioinformatics/comments/107att3/extract_pairwise_alignments_from_sambam_file/

Answer 1

[Istvan Albert]

The tool sam2pairwise does what you need:

https://github.com/mlafave/sam2pairwise