Welcome to the Genome Toolbox! I am glad you navigated to the blog and hope you find the contents useful and insightful for your genomic needs. If you find any of the entries particularly helpful, be sure to click the +1 button on the bottom of the post and share with your colleagues. Your input is encouraged, so if you have comments or are aware of more efficient tools not included in a post, I would love to hear from you. Enjoy your time browsing through the Toolbox.

Sunday, May 5, 2013

Samtools Coverage Depth for Multiple Regions of Interest

Here's some code to use Samtools to extract the sequencing coverage depth from a BAM file for multiple regions of interest as specified in a BED file.  The resulting filename_depth.txt gives coverage data for each base in the region that is in the BAM file.

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