Error while running Catvariants " class main"

MUHAMMADSOHAILRAZAMUHAMMADSOHAILRAZA Beijing Institute of Genomics, CASMember

I am trying combine variants of different chromosomes with same number of samples with following command:

REF=reference.fa
GATK4=/softwares/GATK-3.4-46/GenomeAnalysisTK.jar

java -cp $GATK4/GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.CatVariants \
-R $REF \
-V ALL.chr1_biallelic.vcf \
-V ALL.chr2_biallelic.vcf \
-V ALL.chr3_biallelic.vcf \
-out ALL.WGS.chr.phase3_biallelic.vcf \
-assumeSorted

But i get the following the error:

Error: Could not find or load main class org.broadinstitute.gatk.tools.CatVariants

Could you please help me to fix this?

Thanks

Answers

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