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Old 10-12-2011, 12:38 PM   #1
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Location: Iowa

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Default Extracting reads from BAM files

Hi All,

I am new to samtools and some help will be awesome.

I have BAM files and I have a long list of loci which I want to extract reads for. Basically I want to pass a lot a loci in the regions parameter of samtools view.
I am guessing its a 1 liner code in samtools?

alpesh is offline   Reply With Quote
Old 10-12-2011, 02:59 PM   #2
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Location: San Diego

Join Date: May 2008
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Use BEDTools intersectBed. It can take a bed file of your regions, and a bam file, and return a bam file filtered for only reads that cross one of your reigons.
swbarnes2 is offline   Reply With Quote

bam files, samtools

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