Conpair compatibility with GATK4 latest version

[Huma-Shehwana]

Hi On my previous server, I was able to run Conpair with GATK3.8 but now, on my new server, my java is not compatible with GATK3.8. So I am trying to run Conpair with GATK4.2.3 using the following command but I am continuously getting an error. I would really appreciate your help to resolve this issue.

Command: python3 /DATA/General_Resources/Tools/Conpair/scripts/run_gatk_pileup_for_sample.py -B PRADO_data/7B_dedupraw/S2697Nr36_dedup.bam -O PRADO_data/NTmatch/S2697Nr36_pileup --reference /DATA/peeper_lab/reference_fasta_files/GRCh38.d1.vd1.fa /DATA/General_Resources/Tools/Conpair/data/markers/GRCh38.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.liftover.bed --gatk /DATA/General_Resources/Tools/gatk-4.2.3.0/gatk-package-4.2.3.0-local.jar

Error:

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A USER ERROR has occurred: '-T' is not a valid command.

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