Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

(howto) Compress read data with ReduceReads - DEPRECATED

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie 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

Comments

This discussion has been closed.