The current GATK version is 3.2-2

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Bug Bulletin: The recent 3.2 release fixes many issues. If you run into a problem, please try the latest version before posting a bug report, as your problem may already have been solved.

edited June 2013

#### Objective

Compress the read data in order to minimize file sizes, which facilitates massively multisample processing.

• TBD

### 1. Compress your sequence data

#### Action

Run the following GATK command:

java -jar GenomeAnalysisTK.jar \
-R reference.fa \
-L 20 \


#### Expected Result

This creates a file called reduced_reads.bam containing only the sequence information that is essential for calling variants.

Note that ReduceReads is not meant to be run on multiple samples at once. If you plan on merging your sample bam files, you should run ReduceReads on individual samples before doing so.

Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

Tagged:

• DenmarkPosts: 1Member

Note that ReduceReads is not meant to be run on multiple samples at once. If you plan on merging your sample bam files, you should run ReduceReads on individual samples before doing so.

What about merged bam files from the same sample? I.e. multiple lanes and/or libraries from the same original DNA sample?