Extracting reads from BAM files

[alpesh]

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]

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.