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Hi, may in know is HaplotypeCaller from version3.6 same as version4.1?

There is --nct for HaplotypeCaller in v3.6 to help me speed up the analysis. May i know can if i could replace the HaplotypeCaller from 4.1 to 3.6?

Best Answers


  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    The GATK 4 release promotes the use of Sparktools as the primary method of threading. Each tool that is supported by Spark contains the suffix "Spark". HaplotypeCallerSpark for example, is the Spark version of HaplotypeCaller in GATK 4.0. You can use this tool if you wish to perform threading with HaplotypeCaller.

  • wlaiwlai Member
    @SChaluvadi wondering if the result generated.by spark version are reliable because it is still in beta and i saw from previous forum that it gave different result from non-spark. Not sure hsve the issue resolved yet?
  • wlaiwlai Member
    Thanks for the reply. I have another problem for a while when i run genomicsDBImport.
    Is it okay to ask it at here or in a question?

    The problem:

    A USER ERROR has occurred: Couldn't read file. Error was: Failure while waiting for FeatureReader to initialize with exception: org.broadinstitute.hellbender.exceptions.UserException: Failed to create reader from file:///mnt1/WES_analysis/./LBrun7/LB94.g.vcf.gz

    Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

    My command:
    gatk --java-options "-Xmx4g -Xms4g" -DGATK_STACKTRACE_ON_USER_EXCEPTION=true GenomicsDBImport --genomicsdb-workspace-path my_database -L chr1 --sample-name-map LBrun-map --batch-size 20 --tmp-dir ./tmp --reader-threads 2
    Using GATK jar /home/cruadmin01/installations/gatk-
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx4g -Xms4g -jar /home/cruadmin01/installations/gatk- -DGATK_STACKTRACE_ON_USER_EXCEPTION=true GenomicsDBImport --genomicsdb-workspace-path my_database -L chr1 --sample-name-map LBrun-map --batch-size 20 --tmp-dir ./tmp --reader-threads 2


    A USER ERROR has occurred: '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' is not a valid command.

    Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

    So, I couldnt run GenomicsDBimport and i cant see the Stacktrace. May i have some advice from you to regarding this? Thank you.
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