Reconstruct Alignment changes (read & reference) from CIGAR and MD:Z tag in SAM files

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Pete 2018-5-23

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https://ww2.mathworks.cn/matlabcentral/answers/402171-reconstruct-alignment-changes-read-reference-from-cigar-and-md-z-tag-in-sam-files

关闭： MATLAB Answer Bot 2021-8-20

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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