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(howto) Compress read data with ReduceReads - DEPRECATED

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin
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.

Prerequisites

  • 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

Geraldine Van der Auwera, PhD

Comments

  • pallevillesenpallevillesen DenmarkMember Posts: 1

    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?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,388 admin

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

    Geraldine Van der Auwera, PhD

This discussion has been closed.