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Old 02-23-2011, 11:13 AM   #1
mendl7
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Default Bowtie MD tag format reference

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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Old 02-23-2011, 01:10 PM   #2
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Quote:
Originally Posted by mendl7 View Post
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!
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.
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Old 02-23-2011, 01:47 PM   #3
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Excellent. Thanks for pointing out the sources they are in. Cheers.
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