Dear all
After running CNVDiscoveryPipeline, I want to get the information of genotype for each sample. But when I running GenerateHaploidCNVGenotypes, an error occurred to me (like following).
The version, SVToolkit version 2.00 (build 1696)
Command,
java -cp ${classpath} ${mx} \ org.broadinstitute.sv.apps.GenerateHaploidCNVGenotypes \ -R ref.fasta \ -ploidyMapFile ploidymap.txt \ -genderMapFile sex \ --populationMapFile population \ -vcf gs_cnv.genotypes.vcf.gz \ -estimateAlleleFrequencies true \ -genotypeLikelihoodThreshold 0.001 \ -O $1.duplication.vcf.gz
Exception in thread "main" java.lang.RuntimeException: Error running script /bin/svtoolkit/R/genotyping/estimate_cnv_allele_frequencies.R --dataFile /tmp/tmp_gt_cnv_em_data_7342007552112820353.dat --populationFile /tmp/tmp_gt_cnv_em_pops_6417628549286211376.dat : Error in cnls[samples, ] : subscript out of bounds Calls: main ... processDataFile -> runEMForPopulation -> subsetCNLs Execution halted
Hope for your help.
Best
zhuqing