Does GATK4 contain the tool HaplotypeCaller? I could not find this tool in the latest version of GAT

I have download the latest version of GATK4 from this link:https://github.com/broadinstitute/gatk

After performed ./gradlew localJar and ./gradlew sparkJar, I have built the project successfully and got two jar files which are gatk-package-unspecified-SNAPSHOT-local.jar and gatk-package-unspecified-SNAPSHOT-spark.jar. Then I perform command ./gatk-launch HaplotypeCaller -h, the following error is coming :

Exception in thread "main" org.broadinstitute.hellbender.exceptions.UserException: 'HaplotypeCaller' is not a valid command.

at org.broadinstitute.hellbender.Main.extractCommandLineProgram(Main.java:276)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:140)
at org.broadinstitute.hellbender.Main.main(Main.java:218)

So I have three questions:

1、Does HaplotypeCaller contained in the latest version of GATK4? And when it will be published in GATK4?
2、I find that HaplotypeCallerSpark can be used in gatk-protected(https://github.com/broadinstitute/gatk-protected) , Does it restrict to use without license? And I only find part of tools in the GATK4 protected, does it only provide some license controlled tools?
3、I have tested the GATK pipeline by using best practice of GATK3.7, and what is the best practice of GATK4? can I use the same step of GATK3.7 in GATK4?

THX.

Best Answers

Answers

  • GraceZouGraceZou ChinaMember

    @Geraldine_VdAuwera said:
    1. HaplotypeCaller is in https://github.com/broadinstitute/gatk-protected
    2. Anything in https://github.com/broadinstitute/gatk-protected is subject to the licensing terms that you can find here.
    3. The basic Best Practices are the same in both versions, though the implementation (and some tool names) may be slightly different.

    THX. Then I have another question:

    I use the tool BwaSpark, it has a necessary parameter bwamemIndexImage. How can I get the input of this parameter? Is there any tool help me to do this?

  • GraceZouGraceZou ChinaMember

    @LouisB said:
    BwaSpark is still in a very preliminary state of development and has a lot of issues with it at the moment. Use at your own risk...

    That said, the bwaIndexImage can be created from a set of bwa indexes (there are 5 of them I think: .amb, .ann, .bwt, .pac, .sa) by running the tool BwaIndexImageCreator. Unfortunately, there isn't a way to generate the bwa indexes directly from gatk at the moment. You also have to be sure you generated the index with a version of bwa that is compatible with the version packaged with gatk. The easiest way to do that is to build the bwa mem instance yourself from https://github.com/broadinstitute/gatk-bwamem-jni. We make no guarantee that we'll detect incompatible indexes, you may get a segfault or worse, silently complete with incorrect output.

    Thanks LouisB. I could not find the tool BwaIndexImageCreator, could you tell me how can I download this tool?

  • GraceZouGraceZou ChinaMember

    @LouisB said:
    BwaSpark is still in a very preliminary state of development and has a lot of issues with it at the moment. Use at your own risk...

    That said, the bwaIndexImage can be created from a set of bwa indexes (there are 5 of them I think: .amb, .ann, .bwt, .pac, .sa) by running the tool BwaIndexImageCreator. Unfortunately, there isn't a way to generate the bwa indexes directly from gatk at the moment. You also have to be sure you generated the index with a version of bwa that is compatible with the version packaged with gatk. The easiest way to do that is to build the bwa mem instance yourself from https://github.com/broadinstitute/gatk-bwamem-jni. We make no guarantee that we'll detect incompatible indexes, you may get a segfault or worse, silently complete with incorrect output.

    Now I use gatk-protected, BwaIndexImageCreator is just in there!

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