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paupuigdevall · Jul 3, 2015 · 5cee665 · 5cee665
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diff --git a/...pts/ExpandWorksheetWithMergeWorksheet.jar → ExpandWorksheetWithMergeWorksheet.jar b/...pts/ExpandWorksheetWithMergeWorksheet.jar → ExpandWorksheetWithMergeWorksheet.jar
diff --git a/scripts/Filter_BAMs_NIPT.py → Filter_BAMs_NIPT.py b/scripts/Filter_BAMs_NIPT.py → Filter_BAMs_NIPT.py
diff --git a/scripts/GeneSymbol2BED.pl → GeneSymbol2BED.pl b/scripts/GeneSymbol2BED.pl → GeneSymbol2BED.pl
diff --git a/scripts/GetTranscriptBiotype.pl → GetTranscriptBiotype.pl b/scripts/GetTranscriptBiotype.pl → GetTranscriptBiotype.pl
diff --git a/scripts/InspectComputeJobs.jar → InspectComputeJobs.jar b/scripts/InspectComputeJobs.jar → InspectComputeJobs.jar
diff --git a/scripts/ListFilesOnTape.pl → ListFilesOnTape.pl b/scripts/ListFilesOnTape.pl → ListFilesOnTape.pl
diff --git a/scripts/MD5SumCheck.sh → MD5SumCheck.sh b/scripts/MD5SumCheck.sh → MD5SumCheck.sh
diff --git a/scripts/NIPT/ChiCorrection.R → NIPT/ChiCorrection.R b/scripts/NIPT/ChiCorrection.R → NIPT/ChiCorrection.R
diff --git a/scripts/NIPT/CreateBins.R → NIPT/CreateBins.R b/scripts/NIPT/CreateBins.R → NIPT/CreateBins.R
diff --git a/scripts/NIPT/DetermineBestControl.R → NIPT/DetermineBestControl.R b/scripts/NIPT/DetermineBestControl.R → NIPT/DetermineBestControl.R
diff --git a/scripts/NIPT/DetermineNCV.R → NIPT/DetermineNCV.R b/scripts/NIPT/DetermineNCV.R → NIPT/DetermineNCV.R
diff --git a/scripts/NIPT/DeterminePPV.R → NIPT/DeterminePPV.R b/scripts/NIPT/DeterminePPV.R → NIPT/DeterminePPV.R
diff --git a/scripts/NIPT/DeterminePredictor.R → NIPT/DeterminePredictor.R b/scripts/NIPT/DeterminePredictor.R → NIPT/DeterminePredictor.R
diff --git a/scripts/NIPT/InterChiCorrection.R → NIPT/InterChiCorrection.R b/scripts/NIPT/InterChiCorrection.R → NIPT/InterChiCorrection.R
diff --git a/scripts/NIPT/chi_correction_functions.R → NIPT/chi_correction_functions.R b/scripts/NIPT/chi_correction_functions.R → NIPT/chi_correction_functions.R
diff --git a/scripts/NIPT/create_bins.R → NIPT/create_bins.R b/scripts/NIPT/create_bins.R → NIPT/create_bins.R
diff --git a/scripts/NIPT/determine_predictor.R → NIPT/determine_predictor.R b/scripts/NIPT/determine_predictor.R → NIPT/determine_predictor.R
diff --git a/scripts/NIPT/determine_predictor_functions.R → NIPT/determine_predictor_functions.R b/scripts/NIPT/determine_predictor_functions.R → NIPT/determine_predictor_functions.R
diff --git a/scripts/NIPT/determine_regression_z_score.R → NIPT/determine_regression_z_score.R b/scripts/NIPT/determine_regression_z_score.R → NIPT/determine_regression_z_score.R
diff --git a/...T/test/ChiCorrection/TestChiCorrection.sh → NIPT/test/ChiCorrection/TestChiCorrection.sh b/...T/test/ChiCorrection/TestChiCorrection.sh → NIPT/test/ChiCorrection/TestChiCorrection.sh
diff --git a/...hiCorrection/TestChiCorrection_forward.sh → ...hiCorrection/TestChiCorrection_forward.sh b/...hiCorrection/TestChiCorrection_forward.sh → ...hiCorrection/TestChiCorrection_forward.sh
diff --git a/...40206_u0mm_subopt.BestControlSet.list.tsv → ...40206_u0mm_subopt.BestControlSet.list.tsv b/...40206_u0mm_subopt.BestControlSet.list.tsv → ...40206_u0mm_subopt.BestControlSet.list.tsv
diff --git a/...t.forward.controlfiles.corrected.bins.rds → ...t.forward.controlfiles.corrected.bins.rds b/...t.forward.controlfiles.corrected.bins.rds → ...t.forward.controlfiles.corrected.bins.rds
diff --git a/...m_subopt.forward.corrected.bins.table.tsv → ...m_subopt.forward.corrected.bins.table.tsv b/...m_subopt.forward.corrected.bins.table.tsv → ...m_subopt.forward.corrected.bins.table.tsv
diff --git a/...t.reverse.controlfiles.corrected.bins.rds → ...t.reverse.controlfiles.corrected.bins.rds b/...t.reverse.controlfiles.corrected.bins.rds → ...t.reverse.controlfiles.corrected.bins.rds
diff --git a/...m_subopt.reverse.corrected.bins.table.tsv → ...m_subopt.reverse.corrected.bins.table.tsv b/...m_subopt.reverse.corrected.bins.table.tsv → ...m_subopt.reverse.corrected.bins.table.tsv
diff --git a/...ts/NIPT/test/CreateBins/TestCreateBins.sh → NIPT/test/CreateBins/TestCreateBins.sh b/...ts/NIPT/test/CreateBins/TestCreateBins.sh → NIPT/test/CreateBins/TestCreateBins.sh
diff --git a/...test/CreateBins/TestCreateBins_forward.sh → ...test/CreateBins/TestCreateBins_forward.sh b/...test/CreateBins/TestCreateBins_forward.sh → ...test/CreateBins/TestCreateBins_forward.sh
diff --git a/...test/CreateBins/TestCreateBins_reverse.sh → ...test/CreateBins/TestCreateBins_reverse.sh b/...test/CreateBins/TestCreateBins_reverse.sh → ...test/CreateBins/TestCreateBins_reverse.sh
diff --git a/scripts/NIPT/test/CreateBins/data → NIPT/test/CreateBins/data b/scripts/NIPT/test/CreateBins/data → NIPT/test/CreateBins/data
diff --git a/...ns/output/GoldsStandards_bins_forward.csv → ...ns/output/GoldsStandards_bins_forward.csv b/...ns/output/GoldsStandards_bins_forward.csv → ...ns/output/GoldsStandards_bins_forward.csv
diff --git a/...ns/output/GoldsStandards_bins_forward.pdf → ...ns/output/GoldsStandards_bins_forward.pdf b/...ns/output/GoldsStandards_bins_forward.pdf → ...ns/output/GoldsStandards_bins_forward.pdf
diff --git a/...ns/output/GoldsStandards_bins_reverse.csv → ...ns/output/GoldsStandards_bins_reverse.csv b/...ns/output/GoldsStandards_bins_reverse.csv → ...ns/output/GoldsStandards_bins_reverse.csv
diff --git a/...ns/output/GoldsStandards_bins_reverse.pdf → ...ns/output/GoldsStandards_bins_reverse.pdf b/...ns/output/GoldsStandards_bins_reverse.pdf → ...ns/output/GoldsStandards_bins_reverse.pdf
diff --git a/...BestControl_will_be_removed_from_pipeline → ...BestControl_will_be_removed_from_pipeline b/...BestControl_will_be_removed_from_pipeline → ...BestControl_will_be_removed_from_pipeline
diff --git a/...iCorrection_will_be_removed_from_pipeline → ...iCorrection_will_be_removed_from_pipeline b/...iCorrection_will_be_removed_from_pipeline → ...iCorrection_will_be_removed_from_pipeline
diff --git a/...t/data/testReads/gold_standard_README.txt → ...t/data/testReads/gold_standard_README.txt b/...t/data/testReads/gold_standard_README.txt → ...t/data/testReads/gold_standard_README.txt
diff --git a/scripts/RecodeFRToZero.awk → RecodeFRToZero.awk b/scripts/RecodeFRToZero.awk → RecodeFRToZero.awk
diff --git a/...s/SNP_quality_histograms/functions_bins.R → SNP_quality_histograms/functions_bins.R b/...s/SNP_quality_histograms/functions_bins.R → SNP_quality_histograms/functions_bins.R
diff --git a/...s/SNP_quality_histograms/plot_functions.R → SNP_quality_histograms/plot_functions.R b/...s/SNP_quality_histograms/plot_functions.R → SNP_quality_histograms/plot_functions.R
diff --git a/scripts/SNP_quality_histograms/testcmd.R → SNP_quality_histograms/testcmd.R b/scripts/SNP_quality_histograms/testcmd.R → SNP_quality_histograms/testcmd.R
diff --git a/scripts/SortVCFFilename.py → SortVCFFilename.py b/scripts/SortVCFFilename.py → SortVCFFilename.py
diff --git a/scripts/align-vcf-to-ref.pl → align-vcf-to-ref.pl b/scripts/align-vcf-to-ref.pl → align-vcf-to-ref.pl
diff --git a/scripts/bam_check_for_eof.py → bam_check_for_eof.py b/scripts/bam_check_for_eof.py → bam_check_for_eof.py
diff --git a/scripts/bwa-0.5.8c_patched.tar.gz → bwa-0.5.8c_patched.tar.gz b/scripts/bwa-0.5.8c_patched.tar.gz → bwa-0.5.8c_patched.tar.gz
diff --git a/scripts/change_vcf_filter.pl → change_vcf_filter.pl b/scripts/change_vcf_filter.pl → change_vcf_filter.pl
diff --git a/scripts/checkSubset.pl → checkSubset.pl b/scripts/checkSubset.pl → checkSubset.pl
diff --git a/scripts/check_contamination.pl → check_contamination.pl b/scripts/check_contamination.pl → check_contamination.pl
diff --git a/scripts/check_lane_output.pl → check_lane_output.pl b/scripts/check_lane_output.pl → check_lane_output.pl
diff --git a/scripts/check_output.pl → check_output.pl b/scripts/check_output.pl → check_output.pl
diff --git a/scripts/collect_GoNL_lane_stats.pl → collect_GoNL_lane_stats.pl b/scripts/collect_GoNL_lane_stats.pl → collect_GoNL_lane_stats.pl
diff --git a/...pts/collect_GoNL_sample_coverage_stats.pl → collect_GoNL_sample_coverage_stats.pl b/...pts/collect_GoNL_sample_coverage_stats.pl → collect_GoNL_sample_coverage_stats.pl
diff --git a/scripts/collect_GoNL_sample_stats.pl → collect_GoNL_sample_stats.pl b/scripts/collect_GoNL_sample_stats.pl → collect_GoNL_sample_stats.pl
diff --git a/scripts/collect_alignment_stats.pl → collect_alignment_stats.pl b/scripts/collect_alignment_stats.pl → collect_alignment_stats.pl
diff --git a/scripts/collect_bamIndex_stats.pl → collect_bamIndex_stats.pl b/scripts/collect_bamIndex_stats.pl → collect_bamIndex_stats.pl
diff --git a/scripts/collect_coverage_stats.pl → collect_coverage_stats.pl b/scripts/collect_coverage_stats.pl → collect_coverage_stats.pl
diff --git a/scripts/collect_in_house_samplestats.pl → collect_in_house_samplestats.pl b/scripts/collect_in_house_samplestats.pl → collect_in_house_samplestats.pl
diff --git a/scripts/collect_stats_first_batch.pl → collect_stats_first_batch.pl b/scripts/collect_stats_first_batch.pl → collect_stats_first_batch.pl
diff --git a/scripts/convertBatches.pl → convertBatches.pl b/scripts/convertBatches.pl → convertBatches.pl
diff --git a/scripts/convertDose.py → convertDose.py b/scripts/convertDose.py → convertDose.py
diff --git a/scripts/convertDoseGonl.py → convertDoseGonl.py b/scripts/convertDoseGonl.py → convertDoseGonl.py
diff --git a/scripts/convertPCA.py → convertPCA.py b/scripts/convertPCA.py → convertPCA.py
diff --git a/...ts/convert_beagle_reference_to_impute2.py → convert_beagle_reference_to_impute2.py b/...ts/convert_beagle_reference_to_impute2.py → convert_beagle_reference_to_impute2.py
diff --git a/scripts/convert_snpIDs.pl → convert_snpIDs.pl b/scripts/convert_snpIDs.pl → convert_snpIDs.pl
diff --git a/scripts/copy2grid.pl → copy2grid.pl b/scripts/copy2grid.pl → copy2grid.pl
diff --git a/scripts/countBaseInBed.sh → countBaseInBed.sh b/scripts/countBaseInBed.sh → countBaseInBed.sh
diff --git a/scripts/coverage.R → coverage.R b/scripts/coverage.R → coverage.R
diff --git a/scripts/createBWAandSAMtoolsIndices.pl → createBWAandSAMtoolsIndices.pl b/scripts/createBWAandSAMtoolsIndices.pl → createBWAandSAMtoolsIndices.pl
diff --git a/scripts/createDBSNProdPerChr.pl → createDBSNProdPerChr.pl b/scripts/createDBSNProdPerChr.pl → createDBSNProdPerChr.pl
diff --git a/scripts/createInsertSizePlot.R → createInsertSizePlot.R b/scripts/createInsertSizePlot.R → createInsertSizePlot.R
diff --git a/scripts/createLocalRealignmentIntervals.pl → createLocalRealignmentIntervals.pl b/scripts/createLocalRealignmentIntervals.pl → createLocalRealignmentIntervals.pl
diff --git a/scripts/createSNPTable.R → createSNPTable.R b/scripts/createSNPTable.R → createSNPTable.R
diff --git a/scripts/createSNPTable/createSNPTable.R → createSNPTable/createSNPTable.R b/scripts/createSNPTable/createSNPTable.R → createSNPTable/createSNPTable.R
diff --git a/.../createSNPTable/createSNPTableFunctions.R → createSNPTable/createSNPTableFunctions.R b/.../createSNPTable/createSNPTableFunctions.R → createSNPTable/createSNPTableFunctions.R
diff --git a/scripts/createSNPTable/readCommandLineArgs.R → createSNPTable/readCommandLineArgs.R b/scripts/createSNPTable/readCommandLineArgs.R → createSNPTable/readCommandLineArgs.R
diff --git a/scripts/createVCFfilePerChr.pl → createVCFfilePerChr.pl b/scripts/createVCFfilePerChr.pl → createVCFfilePerChr.pl
diff --git a/scripts/create_coverage_bed.pl → create_coverage_bed.pl b/scripts/create_coverage_bed.pl → create_coverage_bed.pl
diff --git a/scripts/create_interval_bins.pl → create_interval_bins.pl b/scripts/create_interval_bins.pl → create_interval_bins.pl
diff --git a/scripts/create_interval_list.pl → create_interval_list.pl b/scripts/create_interval_list.pl → create_interval_list.pl
diff --git a/scripts/create_interval_listV4.pl → create_interval_listV4.pl b/scripts/create_interval_listV4.pl → create_interval_listV4.pl
diff --git a/scripts/create_per_base_intervals.pl → create_per_base_intervals.pl b/scripts/create_per_base_intervals.pl → create_per_base_intervals.pl
diff --git a/scripts/create_per_base_intervals.sh → create_per_base_intervals.sh b/scripts/create_per_base_intervals.sh → create_per_base_intervals.sh
diff --git a/scripts/ctop → ctop b/scripts/ctop → ctop
diff --git a/scripts/dataTransfer.sh → dataTransfer.sh b/scripts/dataTransfer.sh → dataTransfer.sh
diff --git a/...ts/demultiplex_miseq_illumina_barcoded.pl → demultiplex_miseq_illumina_barcoded.pl b/...ts/demultiplex_miseq_illumina_barcoded.pl → demultiplex_miseq_illumina_barcoded.pl
diff --git a/scripts/extract_info_GATK_variantEval.R → extract_info_GATK_variantEval.R b/scripts/extract_info_GATK_variantEval.R → extract_info_GATK_variantEval.R
diff --git a/scripts/fastqc_report.pl → fastqc_report.pl b/scripts/fastqc_report.pl → fastqc_report.pl
diff --git a/scripts/filterCSV.pl → filterCSV.pl b/scripts/filterCSV.pl → filterCSV.pl
diff --git a/scripts/filterHGMD.pl → filterHGMD.pl b/scripts/filterHGMD.pl → filterHGMD.pl
diff --git a/scripts/filterSingleSampleCalls.pl → filterSingleSampleCalls.pl b/scripts/filterSingleSampleCalls.pl → filterSingleSampleCalls.pl
diff --git a/scripts/filter_BeagleR2.pl → filter_BeagleR2.pl b/scripts/filter_BeagleR2.pl → filter_BeagleR2.pl
diff --git a/scripts/filter_region_and_indvs_from_VCF.pl → filter_region_and_indvs_from_VCF.pl b/scripts/filter_region_and_indvs_from_VCF.pl → filter_region_and_indvs_from_VCF.pl
diff --git a/scripts/flip-vcf-snp.pl → flip-vcf-snp.pl b/scripts/flip-vcf-snp.pl → flip-vcf-snp.pl
diff --git a/scripts/functions_bins.R → functions_bins.R b/scripts/functions_bins.R → functions_bins.R
diff --git a/scripts/gcc_sync.bash → gcc_sync.bash b/scripts/gcc_sync.bash → gcc_sync.bash
diff --git a/scripts/gentrap_graph_seqgc.py → gentrap_graph_seqgc.py b/scripts/gentrap_graph_seqgc.py → gentrap_graph_seqgc.py
diff --git a/scripts/getDedupInfo.R → getDedupInfo.R b/scripts/getDedupInfo.R → getDedupInfo.R
diff --git a/.../getDedupInfo/createDedupTableFunctions.R → getDedupInfo/createDedupTableFunctions.R b/.../getDedupInfo/createDedupTableFunctions.R → getDedupInfo/createDedupTableFunctions.R
diff --git a/scripts/getDedupInfo/getDedupInfo.R → getDedupInfo/getDedupInfo.R b/scripts/getDedupInfo/getDedupInfo.R → getDedupInfo/getDedupInfo.R
diff --git a/scripts/getDedupInfo/out.tex → getDedupInfo/out.tex b/scripts/getDedupInfo/out.tex → getDedupInfo/out.tex
diff --git a/scripts/getDedupInfo/readCommandLineArgs.R → getDedupInfo/readCommandLineArgs.R b/scripts/getDedupInfo/readCommandLineArgs.R → getDedupInfo/readCommandLineArgs.R
diff --git a/scripts/getDedupInfo/run.sh → getDedupInfo/run.sh b/scripts/getDedupInfo/run.sh → getDedupInfo/run.sh
diff --git a/...BXX_L4_AGAGAT.human_g1k_v37.dedup.metrics → ...BXX_L4_AGAGAT.human_g1k_v37.dedup.metrics b/...BXX_L4_AGAGAT.human_g1k_v37.dedup.metrics → ...BXX_L4_AGAGAT.human_g1k_v37.dedup.metrics
diff --git a/...BXX_L4_TAATTT.human_g1k_v37.dedup.metrics → ...BXX_L4_TAATTT.human_g1k_v37.dedup.metrics b/...BXX_L4_TAATTT.human_g1k_v37.dedup.metrics → ...BXX_L4_TAATTT.human_g1k_v37.dedup.metrics
diff --git a/...CXX_L5_AGAGAT.human_g1k_v37.dedup.metrics → ...CXX_L5_AGAGAT.human_g1k_v37.dedup.metrics b/...CXX_L5_AGAGAT.human_g1k_v37.dedup.metrics → ...CXX_L5_AGAGAT.human_g1k_v37.dedup.metrics
diff --git a/...CXX_L5_TAATTT.human_g1k_v37.dedup.metrics → ...CXX_L5_TAATTT.human_g1k_v37.dedup.metrics b/...CXX_L5_TAATTT.human_g1k_v37.dedup.metrics → ...CXX_L5_TAATTT.human_g1k_v37.dedup.metrics
diff --git a/scripts/getDedupInfo/testdata/getdata.sh → getDedupInfo/testdata/getdata.sh b/scripts/getDedupInfo/testdata/getdata.sh → getDedupInfo/testdata/getdata.sh
diff --git a/scripts/getStatistics/GAFpipeline.png → getStatistics/GAFpipeline.png b/scripts/getStatistics/GAFpipeline.png → getStatistics/GAFpipeline.png
diff --git a/scripts/getStatistics/GCCpipeline.png → getStatistics/GCCpipeline.png b/scripts/getStatistics/GCCpipeline.png → getStatistics/GCCpipeline.png
diff --git a/scripts/getStatistics/NiceColumnNames.csv → getStatistics/NiceColumnNames.csv b/scripts/getStatistics/NiceColumnNames.csv → getStatistics/NiceColumnNames.csv
diff --git a/scripts/getStatistics/alignmentFlowchart.pdf → getStatistics/alignmentFlowchart.pdf b/scripts/getStatistics/alignmentFlowchart.pdf → getStatistics/alignmentFlowchart.pdf
diff --git a/scripts/getStatistics/getStatistics.R → getStatistics/getStatistics.R b/scripts/getStatistics/getStatistics.R → getStatistics/getStatistics.R
diff --git a/...ts/getStatistics/getStatisticsFunctions.R → getStatistics/getStatisticsFunctions.R b/...ts/getStatistics/getStatisticsFunctions.R → getStatistics/getStatisticsFunctions.R
diff --git a/...istics/getStatisticsReadCommandLineArgs.R → ...istics/getStatisticsReadCommandLineArgs.R b/...istics/getStatisticsReadCommandLineArgs.R → ...istics/getStatisticsReadCommandLineArgs.R
diff --git a/...getStatistics/variantCallingFlowchart.pdf → getStatistics/variantCallingFlowchart.pdf b/...getStatistics/variantCallingFlowchart.pdf → getStatistics/variantCallingFlowchart.pdf
diff --git a/...ts/getStatistics_Haloplex/GAFpipeline.png → getStatistics_Haloplex/GAFpipeline.png b/...ts/getStatistics_Haloplex/GAFpipeline.png → getStatistics_Haloplex/GAFpipeline.png
diff --git a/...ts/getStatistics_Haloplex/GCCpipeline.png → getStatistics_Haloplex/GCCpipeline.png b/...ts/getStatistics_Haloplex/GCCpipeline.png → getStatistics_Haloplex/GCCpipeline.png
diff --git a/...etStatistics_Haloplex/NiceColumnNames.csv → getStatistics_Haloplex/NiceColumnNames.csv b/...etStatistics_Haloplex/NiceColumnNames.csv → getStatistics_Haloplex/NiceColumnNames.csv
diff --git a/...tatistics_Haloplex/alignmentFlowchart.pdf → ...tatistics_Haloplex/alignmentFlowchart.pdf b/...tatistics_Haloplex/alignmentFlowchart.pdf → ...tatistics_Haloplex/alignmentFlowchart.pdf
diff --git a/...ts/getStatistics_Haloplex/getStatistics.R → getStatistics_Haloplex/getStatistics.R b/...ts/getStatistics_Haloplex/getStatistics.R → getStatistics_Haloplex/getStatistics.R
diff --git a/...tistics_Haloplex/getStatisticsFunctions.R → ...tistics_Haloplex/getStatisticsFunctions.R b/...tistics_Haloplex/getStatisticsFunctions.R → ...tistics_Haloplex/getStatisticsFunctions.R
diff --git a/...loplex/getStatisticsReadCommandLineArgs.R → ...loplex/getStatisticsReadCommandLineArgs.R b/...loplex/getStatisticsReadCommandLineArgs.R → ...loplex/getStatisticsReadCommandLineArgs.R
diff --git a/...tics_Haloplex/variantCallingFlowchart.pdf → ...tics_Haloplex/variantCallingFlowchart.pdf b/...tics_Haloplex/variantCallingFlowchart.pdf → ...tics_Haloplex/variantCallingFlowchart.pdf
diff --git a/scripts/iChip_pos_to_interval_list.pl → iChip_pos_to_interval_list.pl b/scripts/iChip_pos_to_interval_list.pl → iChip_pos_to_interval_list.pl
diff --git a/scripts/import.sh → import.sh b/scripts/import.sh → import.sh
diff --git a/scripts/liftover-bim.pl → liftover-bim.pl b/scripts/liftover-bim.pl → liftover-bim.pl
diff --git a/scripts/makeFinishedAndEnvFiles.sh → makeFinishedAndEnvFiles.sh b/scripts/makeFinishedAndEnvFiles.sh → makeFinishedAndEnvFiles.sh
diff --git a/scripts/makeIndelMask.py → makeIndelMask.py b/scripts/makeIndelMask.py → makeIndelMask.py
diff --git a/scripts/make_compute5_bedfiles.sh → make_compute5_bedfiles.sh b/scripts/make_compute5_bedfiles.sh → make_compute5_bedfiles.sh
diff --git a/scripts/merge_SVs.pl → merge_SVs.pl b/scripts/merge_SVs.pl → merge_SVs.pl
diff --git a/...pts/per_folder/devide_dbSNProd_per_chr.pl → per_folder/devide_dbSNProd_per_chr.pl b/...pts/per_folder/devide_dbSNProd_per_chr.pl → per_folder/devide_dbSNProd_per_chr.pl
diff --git a/scripts/per_folder/devide_vcffile_per_chr.pl → per_folder/devide_vcffile_per_chr.pl b/scripts/per_folder/devide_vcffile_per_chr.pl → per_folder/devide_vcffile_per_chr.pl
diff --git a/scripts/per_folder/index_creator.pl → per_folder/index_creator.pl b/scripts/per_folder/index_creator.pl → per_folder/index_creator.pl
diff --git a/...igner_target_creator_intervals_creator.pl → ...igner_target_creator_intervals_creator.pl b/...igner_target_creator_intervals_creator.pl → ...igner_target_creator_intervals_creator.pl
diff --git a/scripts/plot_coverage.R → plot_coverage.R b/scripts/plot_coverage.R → plot_coverage.R
diff --git a/scripts/plot_cumulative_coverage.R → plot_cumulative_coverage.R b/scripts/plot_cumulative_coverage.R → plot_cumulative_coverage.R
diff --git a/scripts/plot_discordance_matrix.R → plot_discordance_matrix.R b/scripts/plot_discordance_matrix.R → plot_discordance_matrix.R
diff --git a/scripts/plot_functions.R → plot_functions.R b/scripts/plot_functions.R → plot_functions.R
diff --git a/scripts/plot_geno_concordance.R → plot_geno_concordance.R b/scripts/plot_geno_concordance.R → plot_geno_concordance.R
diff --git a/scripts/plot_in-house_cumulative_coverage.R → plot_in-house_cumulative_coverage.R b/scripts/plot_in-house_cumulative_coverage.R → plot_in-house_cumulative_coverage.R
diff --git a/scripts/plot_shared_loci.R → plot_shared_loci.R b/scripts/plot_shared_loci.R → plot_shared_loci.R
diff --git a/scripts/prepareLLGenoData.sh → prepareLLGenoData.sh b/scripts/prepareLLGenoData.sh → prepareLLGenoData.sh
diff --git a/scripts/pull_RNA_Seq_Stats.py → pull_RNA_Seq_Stats.py b/scripts/pull_RNA_Seq_Stats.py → pull_RNA_Seq_Stats.py
diff --git a/scripts/reannotate-vcf-snp-ids.pl → reannotate-vcf-snp-ids.pl b/scripts/reannotate-vcf-snp-ids.pl → reannotate-vcf-snp-ids.pl
diff --git a/scripts/reannotate_immuno.pl → reannotate_immuno.pl b/scripts/reannotate_immuno.pl → reannotate_immuno.pl
diff --git a/scripts/remove_bad_files.pl → remove_bad_files.pl b/scripts/remove_bad_files.pl → remove_bad_files.pl
diff --git a/...uman_All_Exon_V4_S03723314_Padded.sorted.stripped.flanked0-20bp.regionMerged.labelled.bed b/...uman_All_Exon_V4_S03723314_Padded.sorted.stripped.flanked0-20bp.regionMerged.labelled.bed
diff --git a/...uman_All_Exon_V5_S04380110_Padded.sorted.stripped.flanked0-20bp.regionMerged.labelled.bed b/...uman_All_Exon_V5_S04380110_Padded.sorted.stripped.flanked0-20bp.regionMerged.labelled.bed
diff --git a/...10_PADDED_plus_Custom_SCA_0655301.sorted.stripped.flanked0-20bp.regionMerged.labelled.bed b/...10_PADDED_plus_Custom_SCA_0655301.sorted.stripped.flanked0-20bp.regionMerged.labelled.bed
diff --git a/...0_plus_Custom_SCA_0655301/Agilent_SureSelect_Human_Custom_SCA_0655301.sorted.labelled.bed b/...0_plus_Custom_SCA_0655301/Agilent_SureSelect_Human_Custom_SCA_0655301.sorted.labelled.bed