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Thursday, May 9, 2013

Merge Multiple .bam Files

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.

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