Hello, Using "samtools view" I’d like to retrieve reads overlapping a set of regions specified using the “-L” option. I have found however that when regions are specified using this option the index is not used for fast read retrieval. If regions are specified proceeding the bam name IE “samtools view xx.bam chr1:100-105” the index is used. I’m wondering if there is any way to retrieve a large list of regions quickly, using the index, since such a large list can not be passed in the command line. If there currently isn’t, is there any plan to implement the use of the index when the “-L” option is used? I believe this feature would be extremely useful, and would greatly speed up many workflows.
Sincerely, Stephane Castel, PhD Postdoctoral Research Fellow Lappalainen Lab - http://tllab.org New York Genome Center, and Department of Systems Biology Columbia University This electronic message is intended for the use of the named recipient only, and may contain information that is confidential, privileged or protected from disclosure under applicable law. If you are not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, disclosure, dissemination, distribution, copying or use of the contents of this message including any of its attachments is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and destroy all copies of this message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
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