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-   -   Extracting reads from BAM files (http://seqanswers.com/forums/showthread.php?t=14702)

alpesh 10-12-2011 12:38 PM

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?

Thanks,
Alpesh

swbarnes2 10-12-2011 02:59 PM

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.


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