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?