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.

Friday, May 17, 2013

Convert Complete Genomics Data to BAM File

Complete Genomics provides cgatools as a program suite to help manage the data they produce for investigators.  Although still in its beta form, cgatools does provide some functionality for converting evidence dnbs files (.tsv.bz2) to .bam format.  Below is a script that does so, the only caveat being that I can't seem to get the samtools depth command to work with the generated .bam files.

Here are links to documentation and a handy command reference for cgatools.

No comments:

Post a Comment