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how to perform the RealignerTargetCreator when there is not this algorithm anymore

I am trying to use the GATK to realign bam file

Normally I could this this using old version 

java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R hg19.fa -I sorted.bam -o sorted.intervals

Now there is not any GenomeAnalysisTK.jar or RealignerTargetCreator and I am using a newer version of GATK. So if I want to use the older version, I should downgrade my java (it is a pain in Mac) If I want to use the newer one, I don't know how to use it.

I found a command on their web someone was using and it is like this 

gatk RealignerTargetCreator -R hg19.fa -I sorted.bam -nt 6 -o test.intervals

however, I get the following errors 

Exception in thread "main" java.lang.IncompatibleClassChangeError: Inconsistent constant pool data in classfile for class org/broadinstitute/barclay/argparser/CommandLineProgramGroup. Method lambda$static$0(Lorg/broadinstitute/barclay/argparser/CommandLineProgramGroup;Lorg/broadinstitute/barclay/argparser/CommandLineProgramGroup;)I at index 43 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef
    at org.broadinstitute.barclay.argparser.CommandLineProgramGroup.<clinit>(CommandLineProgramGroup.java:19)
    at org.broadinstitute.hellbender.Main.printUsage(Main.java:384)
    at org.broadinstitute.hellbender.Main.extractCommandLineProgram(Main.java:358)
    at org.broadinstitute.hellbender.Main.setupConfigAndExtractProgram(Main.java:182)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:204)
    at org.broadinstitute.hellbender.Main.main(Main.java:291)

when I google the error https://github.com/broadinstitute/gatk/issues/4702

anyone could give me an idea what is going on?

genomics
• 6,571 views • link
written by Learner Learner

Indel Realignment is no longer neccassery and recommended by GATK, if you use the HaplotypeCaller.

So stop wasting your time ;)

fin swimmer

• 1 views • link
written by finswimmer finswimmer

@finswimmer but what about the error I get? why I get those errors when I don't use the Indel Realignment ?

• 1 views • link
written by Learner Learner

In my case, I need the indel Realignment for other variant callers such as Lofreq and CRISP. Also, I get the same exact error even if I just use:

gatk --list
• 0 views • link
written by jfo • jfo

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