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Reconstruct Alignment changes (read & reference) from CIGAR and MD:Z tag in SAM files
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Hi all,
Firstly, I'm not a bioinformatician but have bioinformatics toolbox for work.
I'm writing my own function to interpret a combination of the CIGAR & MD:Z tag from sam files, so I can see the resulting alignment pattern.
Line1: Some READ/REFERENCE OF TGAC'S
Line2: Some alignment pattern of "|| | |||" for example
Line3: Some READ/REFERENCE OF TGAC'S
What I'm wondering is if there is a function that will take the MD and CIGAR and output the identical character positions (maybe even take the read from column 10 in the SAM and give a predicted reference (although insertions would be unknown bases).
Anyone know of such a function for Matlab, either in Bio toolbox or on file-exchange?
Thanks
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