Re: [bedtools-discuss] Using bed intersect with a BAM and a BED file with overlapping regions

[Aaron Quinlan]

Hi Warren,

If your BED file is the -b argument and contains the regions you list, then behavior when using BAM input for the -a argument is to report the alignment only once despite the fact that it overlaps each interval.

- Aaron

quinlanlab.org

On May 13, 2013, at 7:40 AM, warren...@gmail.com wrote:

Hi,

I just wanted to verify that extracting regions from a BAM using a BED file that contains overlaps 

chr1 1 10

chr1 5 20

Will the region 5 - 10 be extracted twice ?

I cant see evidence of this but I just wanted to confirm before going further.

Best,

Warren 

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