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Picard 2.10.2 is now available. As of 2.10.0, Picard supports NovaSeq CBCL data. Download and read release notes at
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GATK to BEAGLE interface

stechenstechen University of PennsylvaniaMember


I'm trying to phase GATK genotype and to impute some SNP calls. Before I could do that, I must convert GATK results to an acceptable BEAGLE input format. What's the difference between VariantsToBeagleUnphased and ProduceBeagleInput? I know the latter outputs a file with genotype likelihoods. Incidentally, using that file didn't work in BEAGLE and produced the following log and error files. Can anyone give any pointers? Thanks in advance!

[stechen@node24 ~]$ more beagle_run_410.o720239
Beagle version 3.3.2 (31 Oct 2011)
Enter "java -jar beagle.jar" for summary of command line arguments.
Start time: 11:59 AM EDT on 07 Aug 2013

Command line: java -Xmx7281m -jar beagle.jar

[stechen@node24 ~]$ more beagle_run_410.e720239
bash: module: line 1: syntax error: unexpected end of file
bash: error importing function definition for `module'
Picked up _JAVA_OPTIONS: -Xms256m -Xmx8G
Exception in thread "main" java.lang.NullPointerException
at phaser.y.a(Unknown Source)
at phaser.y.(Unknown Source)
at phaser.H.a(Unknown Source)
at phaser.v.(Unknown Source)
at phaser.PhaseMain.(Unknown Source)
at phaser.PhaseMain.main(Unknown Source)


Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi there,

    For usage of the Beagle-related tools, we have a presentation that explains it in detail. Have a look at our Guide section, category "Events", under Best Practices Workshop. You'll find several presentations including one on genotype refinement. Let me know if you have trouble finding it. I'd give you a direct link but I'm doing this on a smartphone (which is acting not so smart right now).

    For help with running Beagle software itself, please ask the Beagle maintainers for support.

  • stechenstechen University of PennsylvaniaMember

    Thanks for the info, Geraldine! May I ask how do I reach the Beagle maintainers?

  • stechenstechen University of PennsylvaniaMember
    edited August 2013

    Also, I have indeed seen the workshop slides. Still, I'm wondering what's the difference between VariantsToBeagleUnphased and ProduceBeagleInput?

    Also, in the GATK page, the command is given as "java -Xmx4000m -jar path_to_beagle/beagle.jar like=path_to_beagle_output/beagle_output out=myrun" What if I wanted to use a phased file as the template? It also seems to not work without a marker argument, is that correct?

    Thanks again!

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