R/FirstBB.R

In afrangou/CleanCNA: Calling and recalling subclonal copy number using SNP and SNV information to provide a high quality set of copy number profiles.

# #----------------------#
# # Set up first BB run
# #----------------------#
#

#
# CreateScriptsDirs <- function(resultsdir,participantid,tumourplatekey,normalplatekey,tumourbam,normalbam,gender,project.code,bb1done,ccubeexists) {
#
#         # define gender true false
#         if (gender=="Female") {gendertrue = "FALSE"}
#         if (gender=="Male") {gendertrue = "TRUE"}
#
#         # create overall sample dir
#         participantdir = paste0(resultsdir,participantid)
#         dir.create(participantdir)
#         sampledir = paste0(participantdir,"/tumo",tumourplatekey,"_norm",normalplatekey)
#         dir.create(sampledir)
#
#         # create subdirs & subsubdirs
#         dir.create(paste0(sampledir,"/A-GetAlleleCounts"))
#         dir.create(paste0(sampledir,"/B-RunBAFLogR"))
#         dir.create(paste0(sampledir,"/C-RunGCcorrect"))
#         dir.create(paste0(sampledir,"/D-GenerateImputeInputFromAlleleFrequencies"))
#         dir.create(paste0(sampledir,"/E-RunImpute"))
#         dir.create(paste0(sampledir,"/F-CombineImputeOutputs"))
#         dir.create(paste0(sampledir,"/G-GetHaplotypedBAFs"))
#         dir.create(paste0(sampledir,"/H-CleanUp"))
#         dir.create(paste0(sampledir,"/I-PlotHaplotypedData"))
#         dir.create(paste0(sampledir,"/J-CombineBAFfiles"))
#         dir.create(paste0(sampledir,"/K-SegmentBAFphased"))
#         dir.create(paste0(sampledir,"/L-FitCopyNumber"))
#         dir.create(paste0(sampledir,"/M-CallSubclones"))
#         dir.create(paste0(sampledir,"/N-wrapup"))
#         dir.create(paste0(sampledir,"/O-Postprocessing"))
#         dir.create(paste0(sampledir,"/P-DPC1"))
#         dir.create(paste0(sampledir,"/P-DPC1/DPPrep"))
#         dir.create(paste0(sampledir,"/P-DPC1/DPClust"))
#         dir.create(paste0(sampledir,"/Q-AssessBB1DPC1"))
#         dir.create(paste0(sampledir,"/R-BB2"))
#         dir.create(paste0(sampledir,"/R-BB2/L-FitCopyNumber"))
#         dir.create(paste0(sampledir,"/R-BB2/M-CallSubclones"))
#         dir.create(paste0(sampledir,"/R-BB2/O-Postprocessing"))
#         dir.create(paste0(sampledir,"/S-DPC2"))
#         dir.create(paste0(sampledir,"/S-DPC2/DPPrep"))
#         dir.create(paste0(sampledir,"/S-DPC2/DPClust"))
#         dir.create(paste0(sampledir,"/T-AssessBB2DPC2"))
#         dir.create(paste0(sampledir,"/U-BB3"))
#         dir.create(paste0(sampledir,"/U-BB3/L-FitCopyNumber"))
#         dir.create(paste0(sampledir,"/U-BB3/M-CallSubclones"))
#         dir.create(paste0(sampledir,"/U-BB3/O-Postprocessing"))
#         dir.create(paste0(sampledir,"/V-DPC3"))
#         dir.create(paste0(sampledir,"/V-DPC3/DPPrep"))
#         dir.create(paste0(sampledir,"/V-DPC3/DPClust"))
#         dir.create(paste0(sampledir,"/W-AssessBB3DPC3"))
#         dir.create(paste0(sampledir,"/logs"))
#
#         # create basic config file (parameters will be added later if reruns are required)
#         config=matrix(nrow=34,ncol=1)
#         config[1,1]=paste0("RUN_DIR=",resultsdir)
#         config[2,1]=paste0("LOG_DIR=",sampledir,"/logs/")
#         config[3,1]=paste0("OUTPUT_DIR=",sampledir)
#         config[4,1]=paste0("SAMPLE_PATH=",sampledir)
#         config[5,1]="PIPELINE_DIR=/home/AFrangou/battenberg-lsf-pipeline"
#         config[6,1]=paste0("TUMOURNAME=",tumourplatekey)
#         config[7,1]=paste0("IS_MALE=",gendertrue)
#         config[8,1]=paste0("NORMALNAME=",normalplatekey)
#         config[9,1]=paste0("TUMOURBAM=",tumourbam)
#         config[10,1]=paste0("NORMALBAM=",normalbam)
#         config[11,1]="PLATFORM_GAMMA=1"
#         config[12,1]="PHASING_GAMMA=1"
#         config[13,1]="SEGMENTATION_GAMMA=10"
#         config[14,1]="CLONALITY_DIST_METRIC=0"
#         config[15,1]="ASCAT_DIST_METRIC=1"
#         config[16,1]="MIN_PLOIDY=1.6"
#         config[17,1]="MAX_PLOIDY=4.8"
#         config[18,1]="MIN_RHO=0.13"
#         config[19,1]="MAX_RHO=1.02"
#         config[20,1]="MIN_GOODNESS_OF_FIT=0.63"
#         config[21,1]="BALANCED_THRESHOLD=0.51"
#         config[22,1]="IMPUTEINFOFILE=/home/AFrangou/ALL_100G_phase1integrated_v3_impute/impute_info.txt"
#         config[23,1]="IMPUTE_EXE=/home/AFrangou/impute_v2.3.2_x86_64_static/impute2"
#         config[24,1]="SEED=123"
#         config[25,1]="MAX_CN_STATE=250"
#         config[26,1]="SV_BREAKPOINTS_FILE=NA"
#         config[27,1]="PROBLEMLOCI=/home/AFrangou/probloci_270415.txt"
#         config[28,1]="G1000_PREFIX_HG38=/home/AFrangou/battenberg_1000genomesloci2012_v3_hg38/hg38_alleleFiles_feb22_chr"
#         config[29,1]="G1000_PREFIX_AC_HG38=/home/AFrangou/battenberg_1000genomesloci2012_v3_hg38/hg38_lociFiles_feb22_chr"
#         config[30,1]="G1000_PREFIX=/home/AFrangou/battenberg_1000genomesloci2012_v3/1000genomesAlleles2012_chr"
#         config[31,1]="G1000_PREFIX_AC=/home/AFrangou/runallelecounter/1000genomesloci2012/1000genomesloci2012_chr"
#         config[32,1]="GCCORRECTPREFIX=/home/AFrangou/battenberg_wgs_gc_correction_1000g_v3/1000_genomes_GC_corr_filled_chr_"
#         config[33,1]="MIN_NORMAL_DEPTH=10"
#         config[34,1]="ALLELECOUNTER=/home/AFrangou/bin/alleleCounter"
#         config[35,1]=paste0("PARTICIPANTID=",participantid)
#
#         write.table(config,paste0(sampledir,"/",tumourplatekey,"_configfile.txt"),
#                     quote=F,
#                     col.names=F,
#                     row.names=F)
#
#         # create script for first Battenberg run
#         header=matrix(nrow=51,ncol=1)
#         header[1,1]="#!/usr/bin/env bash"
#         header[2,1]="CONFIG=$1"
#
#         header[4,1]="# Get allele frequencies"
#         header[5,1]="# Tumour"
#         header[6,1]=paste0('bsub -J"GetAlleleFrequenciesTumour_',
#                           tumourplatekey,'[1-23]" -q gecip -P ',project.code,
#                           ' -o ',sampledir,
#                           '/logs/GetAlleleFrequenciesTumour.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/GetAlleleCounts_tumour.sh ',
#                           sampledir,'/',tumourplatekey,'_configfile.txt')
#
#         header[7,1]="# Normal"
#         header[8,1]=paste0('bsub -J"GetAlleleFrequenciesNormal_',
#                           normalplatekey,'[1-23]" -q gecip -P ',project.code,
#                           ' -o ',sampledir,
#                           '/logs/GetAlleleFrequenciesNormal.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/GetAlleleCounts_normal.sh ',
#                           sampledir,'/',tumourplatekey,'_configfile.txt')
#
#         header[10,1]="# Remove 'chr' from alleleCounter output, array"
#         header[11,1]=paste0('bsub -w"done(GetAlleleFrequenciesTumour_',
#                             tumourplatekey,'[1-23]) && done(GetAlleleFrequenciesNormal_',
#                             normalplatekey,'[1-23])" -J"RunRemoveCHR_',tumourplatekey,
#                             '" -q gecip -P ',project.code,
#                             ' -o ',sampledir,'/logs/RemoveCHR.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/RemoveCHR.sh ',
#                             sampledir,'/',tumourplatekey,'_configfile.txt')
#
#         header[13,1]=paste0("# Convert alleleCounter output back to hg37")
#         header[14,1]=paste0('bsub -w"done(RunRemoveCHR_',tumourplatekey,')" -J"RunSwitchback_hg38_to_hg37_',
#                             tumourplatekey,'[1-23]" -q gecip -P ',project.code,
#                            ' -o ',sampledir,'/logs/Switchback_hg38_to_hg37.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/Switchback_hg38_to_hg37.sh ',
#                            sampledir,'/',tumourplatekey,'_configfile.txt')
#
#         header[16,1]="# Get BAF and logR"
#         header[17,1]=paste0('bsub -w"done(RunSwitchback_hg38_to_hg37_',
#                            tumourplatekey,'[1-23])" -R"select[mem>28000] rusage[mem=28000]" -M28000 -J"RunBAFLogR_',
#                            tumourplatekey,'" -q gecip -P ',project.code,
#                            ' -o ',sampledir,'/logs/RunBAFLogR.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/RunBAFLogR.sh ',
#                            sampledir,'/',tumourplatekey,'_configfile.txt')
#
#         header[19,1]='# RunGCCorrect_wgs'
#         header[20,1]=paste0('bsub -w "done(RunBAFLogR_',tumourplatekey,
#                             ')" -R"select[mem>35000] rusage[mem=35000]" -M35000 -J"runGCcorrect_',
#                             tumourplatekey,'" -q gecip -P ',project.code,
#                             ' -o ',sampledir,'/logs/runGCcorrect',tumourplatekey,
#                             '.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/RunGCcorrect_wgs.sh ',
#                             sampledir,'/',tumourplatekey,'_configfile.txt')
#
#         header[22,1]='# Perform phasing'
#         header[23,1]='# GenerateImputeInputFromAlleleFrequencies'
#         header[24,1]=paste0('bsub -w "done(RunSwitchback_hg38_to_hg37_',
#                             tumourplatekey,'[1-23])" -R"select[mem>4000] rusage[mem=4000]" -M4000 -J"GenerateImputeInputs_',
#                             tumourplatekey,'[1-23]" -q gecip -P ',project.code,
#                             ' -o ',sampledir,
#                             '/logs/GenerateImputeInputs.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/GenerateImputeInputFromAlleleFrequencies.sh ',
#                             sampledir,'/',tumourplatekey,'_configfile.txt')
#
#         header[26,1]='# RunImpute'
#         header[27,1]=paste0('bsub -w "done(GenerateImputeInputs_',
#                            tumourplatekey,'[*])" -R"select[mem>8000] rusage[mem=8000]" -M8000 -J"Impute_',
#                            tumourplatekey,'[1-23]" -q gecip -P ',project.code,
#                            ' -o ',sampledir,
#                            '/logs/Impute.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/RunImpute.sh ',
#                            sampledir,'/',tumourplatekey,'_configfile.txt')
#
#         header[29,1]='# CombineImputeOutputs'
#         header[30,1]=paste0('bsub -w"done(Impute_',tumourplatekey,
#                             '[*])" -R"select[mem>4000] rusage[mem=4000]" -M4000 -J"CombineImputeOutputs_',
#                             tumourplatekey,'[1-23]" -q gecip -P ',project.code,' -o ',
#                             sampledir,'/logs/CombineImputeOutputs.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/CombineImputeOutputs.sh ',
#                             sampledir,'/',tumourplatekey,'_configfile.txt')
#
#         header[32,1]='# GetHaplotypeBAFs'
#         header[33,1]=paste0('bsub -w"done(CombineImputeOutputs_',
#                            tumourplatekey,'[*])" -R"select[mem>2000] rusage[mem=2000]" -M2000 -J"GetHaplotypedBAFs_',
#                            tumourplatekey,'[1-23]" -q gecip -P ',project.code,
#                            ' -o ',sampledir,
#                            '/logs/GetHaplotypedBAFs.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/GetHaplotypedBAFs.sh ',
#                            sampledir,'/',tumourplatekey,'_configfile.txt')
#
#         header[35,1]='# CleanUp'
#         header[36,1]=paste0('bsub -w"done(GetHaplotypedBAFs_',
#                            tumourplatekey,'[*])" -J"CleanUp_',
#                            tumourplatekey,'[1-23]" -q gecip -P ',project.code,
#                            ' -o ',sampledir,
#                            '/logs/CleanUp.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/CleanUp.sh ',
#                            sampledir,'/',tumourplatekey,'_configfile.txt')
#
#         header[38,1]='# PlotHaplotypedData'
#         header[39,1]=paste0('bsub -w"done(GetHaplotypedBAFs_',
#                             tumourplatekey,'[*])" -R"select[mem>4000] rusage[mem=4000]" -M4000 -J"PlotHaplotypedData_',
#                             tumourplatekey,'[1-23]" -q gecip -P ',project.code,
#                             ' -o ',sampledir,
#                             '/logs/PlotHaplotypedData.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/PlotHaplotypedData.sh ',
#                             sampledir,'/',tumourplatekey,'_configfile.txt')
#
#         header[41,1]='# CombineBAFfiles'
#         header[42,1]=paste0('bsub -w"done(GetHaplotypedBAFs_',
#                            tumourplatekey,')" -R"select[mem>4000] rusage[mem=4000]" -M4000 -J"CombineBAFfiles_',
#                            tumourplatekey,'" -q gecip -P ',project.code,
#                            ' -o ',sampledir,'/logs/CombineBAFfiles.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/CombineBAFfiles.sh ',
#                            resultsdir,sampledir,'/',tumourplatekey,'_configfile.txt')
#
#         header[44,1]='# Segmentation and copy number calling'
#         header[45,1]=paste0('bsub -w"done(CombineBAFfiles_',
#                             tumourplatekey,')" -R"select[mem>4000] rusage[mem=4000]" -M4000 -J"SegmentBAFphased_',
#                             tumourplatekey,'" -q gecip -P ',project.code,
#                             ' -o ',sampledir,'/logs/SegmentBAFphased.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/SegmentBAFphased.sh ',
#                             sampledir,'/',tumourplatekey,'_configfile.txt')
#
#         header[47,1]=paste0('bsub -w"done(SegmentBAFphased_',
#                            tumourplatekey,') && done(runGCcorrect_',
#                            tumourplatekey,')" -R"select[mem>15900] rusage[mem=15900]" -M15900 -J"FitCopyNumber_',
#                            tumourplatekey,'" -q gecip -P ',project.code,
#                            ' -o ',sampledir,
#                            '/logs/FitCopyNumber.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/FitCopyNumber.sh ',
#                            sampledir,'/',tumourplatekey,'_configfile.txt')
#
#         header[49,1]=paste0('bsub -w"done(FitCopyNumber_',
#                             tumourplatekey,')" -R"select[mem>15900] rusage[mem=15900]" -M15900 -J"CallSubclones_',
#                             tumourplatekey,'" -q gecip -P ',project.code,
#                             ' -o ',sampledir,
#                             '/logs/CallSubclones.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/CallSubclones.sh ',
#                             sampledir,'/',tumourplatekey,'_configfile.txt')
#
#         header[51,1]=paste0('bsub -w"done(CallSubclones_',
#                             tumourplatekey,')" -R"select[mem>500] rusage[mem=500]" -M500 -J"wrapup_',
#                             tumourplatekey,'" -q gecip -P ',project.code,
#                             ' -o ',sampledir,'/logs/wrapup.%J.out /home/AFrangou/battenberg_lsf_pipeline/steps/wrapup.sh ',
#                             sampledir,'/',tumourplatekey,'_configfile.txt')
#
#         header[which(is.na(header[,1])),]=""
#         write.table(header,paste0(sampledir,'/',tumourplatekey,"_submission.sh"),quote=F,col.names=F,row.names=F)
#
#
#         # create script for first DPClust run (does subclones conversion, DPPrep, DPClust)
#
#
#
#
#
#
#
#
#
#         # create overall script to submit whole sample with all (defined) rounds of recall
#         # create script for first Battenberg run
#         header=matrix(nrow=12,ncol=1)
#         header[1,1]="#!/usr/bin/env bash"
#         header[2,1]="CONFIG=$1"
#
#         header[4,1]="# Get allele frequencies"
#         header[5,1]="# Tumour"
#         header[6,1]=paste0('bsub -J"GetAlleleFrequenciesTumour_',
#                            tumourplatekey,'[1-23]" -q gecip -P ',project.code,
#                            ' -o ',sampledir,
#                            '/logs/GetAlleleFrequenciesTumour.%J.%I.out /home/AFrangou/battenberg_lsf_pipeline/steps/GetAlleleCounts_tumour.sh ',
#                            sampledir,'/',tumourplatekey,'_configfile.txt')
#
#
#
#
#
#
# }