CARDIOM Integration test fails with default GATK

[supernifty]

When running the CARDIOM test, the pipeline fails with the default version of GATK (2.3.9):

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: GATK Lite does not support all of the features of the full version: base insertion/deletion recalibration is not supported, please use the --disable_indel_quals argument
##### ERROR ------------------------------------------------------------------------------------------
ERROR: stage failed: Command failed with exit status = 1 :

java -Xmx5g -jar /mnt/ci/jenkins/workspace/Cpipe-Dev/cpipe/tools/gatk/2.3.9/GenomeAnalysisTK.jar  -T BaseRecalibrator  -I align/NA12878_CARDIACM_MUTATED.merge.dedup.realign.bam  -R /mnt/ci/jenkins/workspace/Cpipe-Dev/cpipe/hg19/ucsc.hg19.fasta  -L ../design/combined_target_regions.bed -L ../design/CARDIOM.splice.bed --knownSites /mnt/ci/jenkins/workspace/Cpipe-Dev/cpipe/hg19/dbsnp_138.hg19.vcf  -l INFO  -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate  -o align/NA12878_CARDIACM_MUTATED.merge.dedup.realign.recal_count.counts