View Single Post
Old 06-11-2012, 01:01 PM   #2
adamdeluca
Member
 
Location: Iowa City, IA

Join Date: Jul 2010
Posts: 95
Default

That's what unix pipes are for.

samtools view | myprogram

If you want to write a program to directly access bam files, there is a c library (samtools) and a java library (picard).
adamdeluca is offline   Reply With Quote