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Old 12-19-2011, 11:55 AM   #1
oiiio
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Default Using the .bai to access the BAM

If you knew a range of reads in a BAM file you wanted data for,
say 1:1000-2000, and had its .BAI file- how could you determine the byte range of the .bam file to get?
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Old 12-20-2011, 02:23 AM   #2
maubp
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Normally this is handled by a library (the samtools C API, or Picard for Java).

If you are looking for low level information on the BAI file format in order to write your own code to do this, you should read the text on the BGZF format, virtual offsets, and the BAM indexing format in the SAM/BAM specification - http://samtools.sourceforge.net/SAM1.pdf
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Old 12-20-2011, 12:12 PM   #3
cedance
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The bamtools API provides the functionality for efficient access using BAM and BAI files. This is what most of the tools that inter-operate between SAM and BAM files use in the backend, I suppose. However, this is if you'd want to write a tool yourself. As maubp mentions, why reinvent the wheel? You can just use samtools as follows:

Quote:
samtools view myfile.bam chr:start-end

Last edited by cedance; 12-20-2011 at 12:16 PM.
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