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There is no GenomeAnalysisTK.jar file in gatk package
I downloaded the gatk (GATK18.104.22.168) current version tar file and this works (https://software.broadinstitute.org/gatk/download/):
But I want to do indel realignment and there is no file called GenomeAnalysisTK.jar in the folder. The file name is gatk-22.214.171.124 2, so I am wondering if all these GenomeAnalysisTK.jar based commands are for a previous version.
vr264$ java -jar /Users/vr264/downloads/gatk-126.96.36.199 2/GenomeAnalysisTK.jar
Error: Unable to access jarfile /Users/vr264/downloads/gatk-188.8.131.52 2/GenomeAnalysisTK.jar
How will I run these commands (https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_indels_IndelRealigner.php):
java -jar GenomeAnalysisTK.jar \
-T IndelRealigner \
-R reference.fasta \
-I input.bam \
-known indels.vcf \
-targetIntervals intervalListFromRTC.intervals \