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Picard 2.9.4 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

ReduceReads will no longer be in GATK 3.0

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
edited March 2014 in Announcements

This is an important heads-up regarding the GATK 3.0 release.

The purpose of the ReduceReads algorithm was to enable joint analysis of large cohorts by the UnifiedGenotyper. The new workflow for joint discovery, which involves doing a single-sample pass with the HaplotypeCaller in gVCF mode followed by a joint analysis on multiple sample gVCFs, renders the compression step obsolete.

In addition, based on our most recent analyses, we have come to the conclusion that the quality of variant calls made on BAMs compressed with ReduceReads is inferior to the standard targeted by GATK tools. In comparison, the results obtained with the new workflow are far superior.

For these reasons, we have made the difficult decision to remove the ReduceReads tool from version 3.0 of the toolkit. To be clear, reduced BAMs will NOT be supported in GATK 3.0.

We realize that this may cause some disruption to your existing workflows, and for that we apologize. Please understand that we are driven to provide tools that produce the best possible results. Now that all the data is in, we have found that the best results cannot be achieved with reduced BAMs, so we feel that the best thing to do is to remove this inferior tool from the toolkit, and promote the new tools.

As always we welcome your comments, and we look forward to showing you how the new calling workflow will yield superior results.

Post edited by Geraldine_VdAuwera on
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Comments

  • jpittjpitt Member
    edited March 2014

    Hi @Geraldine_VdAuwera,

    Thanks for the heads up on this! Since I saw this post I've looked around without much success. Is HaplotypeCaller's gVCF and subsequent multi-sample gVCF calling implemented in the current 2.8.1 build of GATK, or do we need to wait until 3.0 is released?

    Also, for multi-sample calling you say that ReducedReads + UnifiedGenotyper perform subotimally compared to HaplotypeCaller + gVCF. Does this mean that the calls obtained from ReducedReads bams are inherently poor? More specifically, are ReducedReads + UnifiedGenotyper calls of much lower quality than regular bams + UnifiedGenotyper calls? Assuming that HaplotypeCaller gVCF is coming in version 3.0, would your team advise against using ReducedReads bams in the meantime?

    Thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @jpitt,

    The gVCF (or reference model) is already implemented in 2.8, though it is further improved in the 3.0 code. However the tools for making joint analyses based on gVCFs of multiple samples (which is what replaces RR+UG) are not yet available; they will be in the new release. Which, if all goes well, will be released tomorrow! So I would advise waiting a day or two for the new version to be available.

    are ReducedReads + UnifiedGenotyper calls of much lower quality than regular bams + UnifiedGenotyper calls?

    It's all relative, but let's say that they are inferior enough (particularly to the results we get with the new method) that we absolutely encourage you to switch over to the new method.

  • BretHBretH University of UtahMember

    How will you be filtering out low-information reads (like pcr duplicates)? Or are these included in the joint varient analysis step?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @BretH,

    We mark duplicates using Picard tools in pre-processing, same as previously. This causes GATK tools to ignore dupes in subsequent analyses.

  • BretHBretH University of UtahMember

    Thank you for your answer.

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