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# (howto) Compress read data with ReduceReads - DEPRECATED

Cambridge, MAMember, Administrator, Broadie
edited May 2015 in Archive

### Please note that this article refers to a method that is no longer recommended as part of the Best Practices!

#### Objective

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

• TBD

#### Steps

1. Compress your sequence data

### 1. Compress your sequence data

#### Action

Run the following GATK command:

java -jar GenomeAnalysisTK.jar \
-T ReduceReads \
-R reference.fa \
-I recal_reads.bam \
-L 20 \
-o reduced_reads.bam


#### 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
Tagged:

## Comments

• DenmarkMember

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?

• Cambridge, MAMember, Administrator, Broadie

Merged bams from the same sample are okay to reduce, yes.

This discussion has been closed.