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Old 01-08-2019, 04:01 PM   #1
touchsk
Junior Member
 
Location: San Francisco, CA

Join Date: Aug 2015
Posts: 7
Default read pairs to fragment coordinates

Hi All,

I have a bam file from the alignment of paired-end NGS data to the human genome. Most of these read-pairs are non-overlapping. Is there any tool that takes this bam as input and provides the merged coordinates from the pairs.

Eg:
Read1-FWD: chr1 1 20
Read1-REV: chr1 80 100

Result: chr1 1 100

If only one read is aligned, then ignore its mate. If the alignment is on opposite strand, reverse for that.

I know a lot of tools estimate fragment size, but do they output results like above as well? I can write a quick script for this, but was wondering if something was already available.
Many thanks.
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