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tgen / pegasusPipe

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update vcfMerger and cna steps with bed files for AHCCC #12

Closed tgenahmet closed 7 years ago

tgenahmet commented 7 years ago

From Austin's email:

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