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.

ReduceReads problem

xdzperfectxdzperfect Beijing Institute of genomicsMember

Dear GATK team:
recently ,I using GATK(version 3.4-0-g7e26428) to do ReduceReads,I got the outcome:

ERROR MESSAGE: Walker ReduceReads is no longer available in the GATK; it has been deprecated since version 3.0 (use recommended best practices pipeline with the HaplotypeCaller)

from that I know that the ReduceReads Walker is no longer available, but you know after doing BQSR,the outcome bam file is nearly two times biger than before doing BQSR . So I want to use the ReduceReads command to the BQSR outcome bam file;
next, I do some research to downlaod earlier version of GATK form "http://gatkforums.broadinstitute.org/",but I couldn't find one, Could you give me an earlier version of GATK,(before version3.0,maybe 2.8?or2.6? is ok)
thank you!


Best Answer


  • xdzperfectxdzperfect Beijing Institute of genomicsMember
Sign In or Register to comment.