GenomeSTRiP v2.0 CNV calling

Hi Bob,

I upgraded to version 2 and ran my samples with a 30 background population samples from 1000G for DEL discovery. I know that SVToolkit now calls deletions and copy number variation, my question is; how do I run CNV discovery. Here are my commands;

java -cp ${classpath} ${mx} \ org.broadinstitute.gatk.queue.QCommandLine \ -S ${SV_DIR}/qscript/SVPreprocess.q \ -S ${SV_DIR}/qscript/SVQScript.q \ -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \ -cp ${classpath} \ -configFile ${SV_DIR}/conf/genstrip_parameters.txt \ -tempDir ${SV_TMPDIR} \ -R data/human_g1k_v37.fasta \ -genomeMaskFile data/human_g1k_v37.mask.100.fasta \ -ploidyMapFile data/humgen_g1k_v37_ploidy.map \ -copyNumberMaskFile data/cn2_mask_g1k_v37.fasta \ -genderMapFile data/geneder1000GandMysamples.map \ -runDirectory ${runDir} \ -md ${runDir}/metadata \ -reduceInsertSizeDistributions true \ -bamFilesAreDisjoint true \ -computeGCProfiles true \ -jobLogDir ${runDir}/logs \ -I ${bamList} \ -run \
java -cp ${classpath} ${mx} \ org.broadinstitute.gatk.queue.QCommandLine \ -S ${SV_DIR}/qscript/SVDiscovery.q \ -S ${SV_DIR}/qscript/SVQScript.q \ -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \ -cp ${classpath} \ -configFile ${SV_DIR}/conf/genstrip_parameters.txt \ -tempDir ${SV_TMPDIR} \ -R data/human_g1k_v37.fasta \ -genomeMaskFile data/human_g1k_v37.mask.100.fasta \ -genderMapFile data/geneder1000GandMysamples.map \ -runDirectory ${runDir} \ -md ${runDir}/metadata \ -jobLogDir ${runDir}/logs \ -minimumSize 100 \ -maximumSize 1000000 \ -suppressVCFCommandLines \ -I ${bamList} \ -O ${sites} \ -run \
java -cp ${classpath} ${mx} \ org.broadinstitute.gatk.queue.QCommandLine \ -S ${SV_DIR}/qscript/SVGenotyper.q \ -S ${SV_DIR}/qscript/SVQScript.q \ -gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \ --disableJobReport \ -cp ${classpath} \ -configFile ${SV_DIR}/conf/genstrip_parameters.txt \ -tempDir ${SV_TMPDIR} \ -R data/human_g1k_v37.fasta \ -genomeMaskFile data/human_g1k_v37.mask.100.fasta \ -ploidyMapFile data/humgen_g1k_v37_ploidy.map \ -genderMapFile data/geneder1000GandMysamples.map \ -runDirectory ${runDir} \ -md ${runDir}/metadata \ -jobLogDir ${runDir}/logs \ -I ${bamList} \ -vcf ${sites} \ -O ${genotypes} \ -run

Would you please let me know what should I do to run CNV calling! And let me know if I did anything wrong in my DEL calling.

Thank you so much,
Reza