Does anyone know of a good source for understanding the alignment description format of Bowtie's MD tag? I'm trying to work out a parser to give me a simple alignment of reference/read from this information. Thanks!
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You can take a look at the source code within SAMtools for creating the MD tag (bam_md.c) or within the PERL SAM module (http://search.cpan.org/~lds/Bio-SamT.../Bio/DB/Sam.pm). Both will show you how to recover the reference sequence using the MD tag and the cigar.Originally posted by mendl7 View Post -
Excellent. Thanks for pointing out the sources they are in. Cheers.Comment
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