I had multiple .bam files from different subjects I wanted to merge into one master .bam file. It seemed like Samtools would easily convert these files using the merge option, but after reading a few online posts there looks like there are some issues with creating an appropriate header for the new merged .bam file from all the original .bam files. Picard seemed to be the optimal method to do this. Here's some code that uses Picard to merge multiple .bam files.
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.