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Old 08-14-2012, 07:21 AM   #1
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Join Date: Mar 2012
Posts: 11
Question Extract aligned sequence coordinates from SAM or BAM file

I have a Illumina sequence reads which I mapped to HG19 using BWA. Resulting BAM file is indexed and sorted. Now what I want is to identify the region of alignment. Let me give an example, on chromosome 1 starting from base 1 to 10000, there are many reads aligned and then there is no any read aligned from 10000 to 20000 and then again from 20000 to 30000 there are many reads aligned and so on...

I want an output like
chr1 1 10000
chr1 20000 30000

I searched for tools doing similar functions but didn't find anything.
Any help will be really appreciated.

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