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Extract alignment in fasta format from BAM/SAM file

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.

alignment bam
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updated by Istvan Albert Istvan Albert • written by SaltedPork SaltedPork

1 answer

The tool sam2pairwise does what you need:

https://github.com/mlafave/sam2pairwise

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written by Istvan Albert Istvan Albert

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