needs to be updated in the vcfMerger.sh script for each pipeline
VCF_Merger_Bed_File: /home/tgenref/pecan/annotations/exome_capture/Agilent_ClearSeq_Beta_ComprehensiveCancer/Agilent_ClearSeq_Beta_ComprehensiveCancer_hs37d5_GRCh37.74_Targets_intersect_sorted.bed
VCF_Merger_Padded_Bed_File: /home/tgenref/pecan/annotations/exome_capture/Agilent_ClearSeq_Beta_ComprehensiveCancer/Agilent_ClearSeq_Beta_ComprehensiveCancer_hs37d5_GRCh37.74_PaddedTargets_intersect_sorted_padded100.bed
goes in to cna.sh for each pipeline
NonMatched_Tumor_CN_Padded_filter: /home/tgenref/pecan/annotations/CN_filter/Agilent_ClearSeq_Beta_ComprehensiveCancer/Agilent_ClearSeq_Beta_ComprehensiveCancer_hs37d5_Padded_DGV_1kg.cna.bed
From Austin's email: