Is it possible to generate variants per read from a SAM/BAM file

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David Roe
David Roe on 5 Feb 2015
Given reads aligned to a reference in a SAM/BAM file, I would like to generate the variants (indels and SNPS) for each read. Can anyone offer suggestions on operations that may support this? It seems like I have parse the reference and read using the CIGAR string. I'm hoping there may already be some code to help.

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