first commit public branch

Extract_PharmGKB_Variants.sh

+HLASCAN=''
+SNPEFF=''
+
+#todo Dowload
+#https://api.pharmgkb.org/v1/download/file/data/clinicalAnnotations.zip
+#change star notation by dbsnp notation with CPIC recommandations or PharmVar website
+
+#data test
+#wget https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/Nebraska_NA12878_HG001_TruSeq_Exome/NIST-hg001-7001-b-gatk.vcf
+
+#HLASCAN
+python2.7 $HLASCAN/HLAscan.v1.0.Files/hla-paper/haplo_scan_v4.0-hla.py $BAMFILE $HLASCAN/HLAscan.v1.0.Files/hla-ref-5gene/gene_list HLAscan_result/
+
+#Annotate VCF File
+bash -o pipefail  -c "java -Xmx4g -jar $SNPEFF/SnpSift.jar annotate pharmgkb_v2.vcf $VCF > ${VCF}_annot"
+
+#create HTML
+python2.7 create_html.py -v ${VCF}_annot -h HLAscan_result/Report -b $BAMFILE -t tableau_pharmgkb.tsv -o Report.html
+

Master.sh

-#!/bin/bash
-
-### GAD PIPELINE ###
-## Master.sh
-## Version : 1.0
-## Description : process pharmacoAnnot for exome data
-## Usage : qsub -v ANALYSISDIR=<path to the analysis dir>,CONFIGFILE=<path to the config file>,PHARMCONFIG=<path to the config_pharm file> Master.sh
-## Output : no standard output
-## Requirements : Require pipeline scripts
-
-## Author : Simon.verdez@u-bourgogne.fr
-## Creation Date : 20180725
-## Last revision date : 20180725
-## Known bugs : None.
-
-#$ -N Master
-#$ -q batchbm
-#$ -pe smp 1
-#$ -V
-
-
-#Logging
-logbasename=$(date +"%F_%H-%M-%S")
-vcfbasename=$(date +"%F")
-reportbasename=$(date +"%F")
-
-
-if [ -z ${LOGFILE} ]
-then
-    LOGFILE=PharmAnnot.$logbasename.log
-fi
-exec 1>> $LOGFILE 2>&1
-
-# Mandatory arguments
-if [ -z ${ANALYSISDIR} ]
-then
-    echo "ANALYSISDIR was not defined : execution stopped"
-    exit 1
-fi
-
-if [ -z ${CONFIGFILE+x} ]
-then
-    echo "Config file not provided by the user. You need it to run this script. Stopping execution."
-    exit
-fi
-
-if [ -z ${PHARMCONFIG+x} ]
-then
-    echo "Config file not provided by the user. You need it to run this script. Stopping execution."
-    exit
-fi
-
-
-#Usefull variables
-PIPELINEBASE=`grep "pipelinebase" $PHARMCONFIG | cut -f2`
-TSVFILE=`grep "pharmagktab" $PHARMCONFIG | cut -f2`
-PHARMGKB=`grep "pharmagkbase" $PHARMCONFIG | cut -f2`
-OMIM=`grep "omim" $PHARMCONFIG | cut -f2`
-HLALIST=`grep "HLAlist" $PHARMCONFIG | cut -f2`
-HEADER=`grep "header" $PHARMCONFIG | cut -f2`
-REF=`grep "reference" $PHARMCONFIG | cut -f2`
-
-# python path for proper execution of python
-PYTHONPATH=$PIPELINEBASE/common:/work/gad/shared/bin/lib/python_2.7/lib/python2.7/site-packages:/work/gad/shared/bin/miniconda2/lib/python2.7/site-packages/
-export PYTHONPATH
-
-# Sample list
-samples=`find -L $ANALYSISDIR/ -maxdepth 1 -mindepth 1 -type d | xargs -l basename`
-
-# Batch sample list
-if [ -e $ANALYSISDIR/batch.list ]
-then
-    rm $ANALYSISDIR/batch.list
-fi
-find -L $ANALYSISDIR/ -maxdepth 1 -mindepth 1 -type d | xargs -l basename >> $ANALYSISDIR/batch.list
-
-HLAscan:
-# HLA genotyping
-echo "### Execute HLAscan ###"
-echo "Start : $(date +"%F_%H-%M-%S")"
-for currentSample in $samples
-do
-    echo "Command : qsub -pe smp 1 -N HLAscan_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.dedup.bam,OUTPUTFILE=$ANALYSISDIR/$currentSample/HLAscan,GeneList=$GL,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_HLAscan.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/haplo_scan.sh"
-#    qsub -q batch -pe smp 1 -N HLAscan_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v BAM=$ANALYSISDIR/$currentSample/$currentSample.dedup.bam,SORTIE=$ANALYSISDIR/$currentSample/HLAscan,GeneList=$GL,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_HLAscan.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/haplo_scan.sh
-done
-echo "End : $(date +"%F_%H-%M-%S")"
-
-varcallSNP:
-# Variant calling first step
-echo "### Variant calling SNP first step ###"
-echo "Start : $(date +"%F_%H-%M-%S")"
-for currentSample in $samples
-do
-    echo "Command : qsub -pe smp 1 -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -N varcallSNP_${currentSample} -v INPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.raw.vcf,PHARMGKB=$PHARMGKB,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcallSNP.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/annotate_variants_pharmAnnot.sh"
-    qsub -q batch -pe smp 1 -N varcallSNP_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.raw.vcf,PHARMGKB=$PHARMGKB,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcallSNP.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/annotate_variants_pharmAnnot.sh
-done
-echo "End : $(date +"%F_%H-%M-%S")"
-
-varcallCNV:
-# Variant calling second step
-echo "### Variant calling CNV second step ###"
-echo "Start : $(date +"%F_%H-%M-%S")"
-for currentSample in $samples
-do
-    cnvfile=`ls -lht $ANALYSISDIR/$currentSample/ | grep "\.annot.tsv" | head -1 | awk '{print $9}'`
-    echo "Command : qsub -pe smp 1 -N varcallCNV_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE=$ANALYSISDIR/$currentSample/$cnvfile,PHARMGKB=$TSVFILE,OMIM=$OMIM,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcallCNV.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/wrapper_tsv2vcf.sh"
-    qsub -q batch -pe smp 1 -N tsv2vcf_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE=$ANALYSISDIR/$currentSample/$cnvfile,PHARMGKB=$TSVFILE,OMIM=$OMIM,REF=$REF,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcallCNV.$logbasenameCNV.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/wrapper_tsv2vcf.sh
-done
-echo "End : $(date +"%F_%H-%M-%S")"
-
-createHTML:
-# Generate a HTML report_vcf
-echo "### Generate HTML report ###"
-echo "Start : $(date +"%F_%H-%M-%S")"
-for currentSample in $samples
-do
-    echo "Command : qsub -pe smp 1 -hold_jid varcallCNV_${currentSample},varcallSNP_${currentSample},HLAscan_${currentSample} -N createHTML_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v VCF_SNP=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,VCF_CNV=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,REPORTFILE=$ANALYSISDIR/$currentSample/HLAscan/Report,BAMFILE=$ANALYSISDIR/$currentSample/$currentSample.dedup.bam,TSVFILE=$TSVFILE,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.html,LOGFILE=$ANALYSISDIR/$currentSample/logs/create_html.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/wrapper_create_html.sh"
-    qsub -q batch -pe smp 1 -hold_jid varcallCNV_${currentSample},varcallSNP_${currentSample},HLAscan_${currentSample} -N createHTML_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v VCF_SNP=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,VCF_CNV=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,REPORTFILE=$ANALYSISDIR/$currentSample/HLAscan/Report,BAMFILE=$ANALYSISDIR/$currentSample/$currentSample.dedup.bam,TSVFILE=$TSVFILE,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.html,LOGFILE=$ANALYSISDIR/$currentSample/logs/create_html.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/wrapper_create_html.sh
-done
-echo "End : $(date +"%F_%H-%M-%S")"
-
-MergeVCF:
-#merge vcf fies
-echo "### Merge VCF files"
-echo "Start : $(date +"%F_%H-%M-%S")"
-for currentSample in $samples
-do
-    echo "Command : qsub -pe smp 1 -hold_jid varcallCNV_${currentSample},varcallSNP_${currentSample} -N mergeVCF_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE1=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,INPUTFILE2=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,REF=$REF,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.merge.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/merge_file.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/merge_GATK.sh"
-    qsub -q batch -pe smp 1 -hold_jid varcallCNV_${currentSample},varcallSNP_${currentSample} -N mergeVCF_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE1=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,INPUTFILE2=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,REF=$REF,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.merge.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/merge_file.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/merge_GATK.sh
-done
-echo "End : $(date +"%F_%H-%M-%S")"

VCF_tools.py

-class VCF_CNV:
-
-    def __init__(self):
-        self.CHROM = 0
-        self.POS = 0
-        self.ID = "."
-        self.REF = "."
-        self.ALT = "."
-        self.QUAL = 6
-        self.FILTER = "PASS"
-        self.SVTYPE = None
-        self.END = 0
-        self.SVLEN = 0
-        self.CIPOS = "0,0"
-        self.CIEND = "0,0"
-        self.GENE = "."
-        self.FORMAT = "GT:GQ"
-        self.SAMPLE = ".:0"
-
-    def __repr__(self):
-        vcf = "{}\t{}\t{}\t{}\t{}\t{}\t{}\tSVTYPE={};END={};SVLEN={};CIPOS={};CIEND={};GENE={}\t{}\t{}".format(self.CHROM,self.POS,self.ID,self.REF,self.ALT,self.QUAL,self.FILTER,self.SVTYPE,self.END,self.SVLEN,self.CIPOS,self.CIEND,self.GENE,self.FORMAT,self.SAMPLE)
-        return vcf
-
-def create_header():
-    header="""##fileformat=VCFv4.2
-##reference=hg19
-##INFO=<ID=BKPTID,Number=1,Type=String,Description="ID of the assembled alternate allele in the assembly file">
-##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
-##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
-##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
-##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
-##INFO=<ID=HOMSEQ,Number=1,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
-##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
-##INFO=<ID=MEINFO,Number=4,Type=String,Description="Mobile element info of the form NAME,START,END,POLARITY">
-##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
-##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
-##INFO=<ID=GENE,Number=1,Type=String,Description="Involved genes">
-##ALT=<ID=DEL,Description="Deletion">
-##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
-##ALT=<ID=DEL:ME:L1,Description="Deletion of L1 element">
-##ALT=<ID=DUP,Description="Duplication">
-##ALT=<ID=DUP:TANDEM,Description="Tandem Duplication">
-##ALT=<ID=INS,Description="Insertion of novel sequence">
-##ALT=<ID=INS:ME:ALU,Description="Insertion of ALU element">
-##ALT=<ID=INS:ME:L1,Description="Insertion of L1 element">
-##ALT=<ID=INV,Description="Inversion">
-##ALT=<ID=CNV,Description="Copy number variable region">
-##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype quality">
-##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
-##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
-##contig=<ID=chrM,length=16571>
-##contig=<ID=chr1,length=249250621>
-##contig=<ID=chr2,length=243199373>
-##contig=<ID=chr3,length=198022430>
-##contig=<ID=chr4,length=191154276>
-##contig=<ID=chr5,length=180915260>
-##contig=<ID=chr6,length=171115067>
-##contig=<ID=chr7,length=159138663>
-##contig=<ID=chr8,length=146364022>
-##contig=<ID=chr9,length=141213431>
-##contig=<ID=chr10,length=135534747>
-##contig=<ID=chr11,length=135006516>
-##contig=<ID=chr12,length=133851895>
-##contig=<ID=chr13,length=115169878>
-##contig=<ID=chr14,length=107349540>
-##contig=<ID=chr15,length=102531392>
-##contig=<ID=chr16,length=90354753>
-##contig=<ID=chr17,length=81195210>
-##contig=<ID=chr18,length=78077248>
-##contig=<ID=chr19,length=59128983>
-##contig=<ID=chr20,length=63025520>
-##contig=<ID=chr21,length=48129895>
-##contig=<ID=chr22,length=51304566>
-##contig=<ID=chrX,length=155270560>
-##contig=<ID=chrY,length=59373566>
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	dijex
-"""
-    return header

analysis_config.tsv

-pipelinebase	/work/gad/shared/pipeline/pharmacogen_test/pharmAnnot
-pythonbin	/work/gad/shared/bin/miniconda2/bin/python
-GATKbase	/work/gad/shared/bin/GATK_3.7
-javacmd	/soft/java/jdk_x64/bin/java
-picardbase	/work/gad/shared/bin/PICARD_2.4.1
-temporary_dir	/work/gad/shared/tmp/
-reference	/work/gad/shared/pipeline/hg19/index/hg19_essential.fa
-refdict	/work/gad/shared/pipeline/hg19/index/hg19_essential.dict
-refdir	/work/gad/shared/pipeline/hg19/index
-dbsnp	/work/gad/shared/pipeline/hg19/clinvar/dbsnp.vcf
-mainqueue	batch
-autosubqueue	batchbm
-bwacmd	/work/gad/shared/bin/bwa-0.7.15
-fastqccmd	/work/gad/shared/bin/FastQC_0.11.4/fastqc
-fastqc_config	/work/gad/shared/bin/FastQC_0.11.4/Configuration/limits.txt
-trimmomatic	/work/gad/shared/bin/Trimmomatic-0.35/trimmomatic-0.35.jar
-adapters_file	/work/gad/shared/bin/Trimmomatic-0.35/adapters/TruSeq3-PE-All.fa
-samtools	/work/gad/shared/bin/samtools-1.5/
-igvtools	/work/gad/shared/bin/IGVTools_2.3.67/igvtools.jar
-targetlist	/work/gad/shared/pipeline/hg19/targets/
-refseqlist	/work/gad/shared/pipeline/hg19/refseq/refseq.cds.2bp.hg19.with_genes.interval_list
-refseqgenelist	/work/gad/shared/pipeline/hg19/refseq/genetrack.hg19.sorted.refseq
-controlfile	/work/gad/shared/pipeline/samples/control_100_samples.g.vcf
-email	emilie.tisserant@u-bourgogne.fr
-clinvar_vcf	/work/gad/shared/pipeline/hg19/clinvar/clinvar.vcf
-cosmic_vcf	/work/gad/shared/pipeline/hg19/cosmic/CosmicCodingMuts.vcf
-omim_list	/work/gad/shared/pipeline/hg19/omim/OMIM2.list
-acmg_list	/work/gad/shared/pipeline/hg19/omim/ACMG.list
-common_list	/work/gad/shared/pipeline/hg19/clinvar/common.list
-ssa_nb_files	10
-tabixpath	/work/gad/shared/bin/htslib-1.3/bin/tabix
-kaviar	/work/gad/shared/pipeline/hg19/kaviar/Kaviar-160204-Public-hg19.vcf.gz
-regulomedb	/work/gad/shared/pipeline/hg19/regulomeDB/RegulomeDB.dbSNP141.txt.gz
-targetscan	/work/gad/shared/pipeline/hg19/targetscan/Predicted_Targets.hg19.bed
-cytobands	/work/gad/shared/pipeline/hg19/cnv/cytobands.tsv
-dgv_variants	/work/gad/shared/pipeline/hg19/cnv/GRCh37_hg19_variants_2015-07-23.txt.gz
-cnv_map	/work/gad/shared/pipeline/hg19/cnv/Stringent.hg19.2015-02-03.txt.gz
-isca_benign_cnv	/work/gad/shared/pipeline/hg19/cnv/iscaBenign.txt.gz
-isca_pathogenic_cnv	/work/gad/shared/pipeline/hg19/cnv/iscaPathogenic.txt.gz
-devdelay_control_cnv	/work/gad/shared/pipeline/hg19/cnv/cnvDevDelayControl.txt.gz
-devdelay_case_cnv	/work/gad/shared/pipeline/hg19/cnv/cnvDevDelayCase.txt.gz
-clingen_dosage_sensitive_gene	/work/gad/shared/pipeline/hg19/cnv/ClinGen_gene_curation_list.tsv
-xhmmbin	/work/gad/shared/bin/xhmm_1.0/xhmm
-xhmmparams	/work/gad/shared/pipeline/hg19/cnv/xhmm_params.txt
-cnvtarget	/work/gad/shared/pipeline/hg19/cnv/cnv_targets_refseq_only_coding_exon_2bp.hg19.list
-targetgc	/work/gad/shared/pipeline/hg19/cnv/cnv_targets_refseq_only_coding_exon_2bp.hg19_GC.txt
-docmatrix	/work/gad/shared/pipeline/hg19/cnv/ALL.CNV.RD.txt
-extremegc	/work/gad/shared/pipeline/hg19/cnv/extreme_gc_targets.txt
-lowcomplexity	/work/gad/shared/pipeline/hg19/cnv/low_complexity_targets.txt
-controlfreec	/work/gad/shared/bin/ControlFreeC
-gemMappabilityFile	/work/gad/shared/pipeline/hg19/cnv/out100m1_hg19.gem
-chrLenFile	/work/gad/shared/pipeline/hg19/index/hg19.len
-chrFiles	/work/gad/shared/pipeline/hg19/index/chr/
-lumpybase	/work/gad/shared/bin/lumpy/lumpy-sv-master/
-mapabilitybedgraph	/work/gad/shared/pipeline/hg19/cnv/wgEncodeCrgMapabilityAlign100mer_no_uniq.bedgraph
-blacklistfile	/work/gad/shared/pipeline/hg19/cnv/wgEncodeDacMapabilityConsensusExcludable.txt
-repeatmasker	/work/gad/shared/pipeline/hg19/cnv/UCSC_rmsk.hg19.sort.bed.gz
-bedtools	/work/gad/shared/bin/bedtools
-nist_bed	/work/gad/shared/pipeline/hg19/nist/agilent_CRE.refseq_cds.NA12878_GIAB_highconf.intersect.hg19.bed
-nist_vcf	/work/gad/shared/pipeline/hg19/nist/NA12878_GIAB_highconf.agilent.refseq.intersect.vcf
-hg19gtf	/work/gad/shared/pipeline/hg19/refseq/hg19.refseq.with_genes.gtf
-star2	/work/gad/shared/bin/STAR-2.5.2b/source
-circosconfdir	/work/gad/shared/pipeline/hg19/circos/
-circosbin	/work/gad/shared/bin/circos-0.69-2/bin/circos
-rscript	/soft/R/3.2.3/intel/13.1.3/bin/Rscript
-snpeffbase	/work/gad/shared/bin/snpEff
-exacvcf	/work/gad/shared/pipeline/hg19/ExAC/ExAC.r0.3.1.sites.vep.vcf.gz
-exacscores	/work/gad/shared/pipeline/hg19/ExAC/fordist_cleaned_exac_r03_march16_z_pli_rec_null_data.txt
-dbnsfp	/work/gad/shared/bin/snpEff/data/dbNSFP/dbNSFP2.9.txt.gz
-gnomadex	/work/gad/shared/pipeline/hg19/ExAC/gnomad.exomes.r2.0.2.sites.vcf.gz
-gnomadge	/work/gad/shared/pipeline/hg19/ExAC/gnomad.genomes.r2.0.2.sites.vcf.gz
-gnomadchr	/work/gad/shared/pipeline/hg19/ExAC/gnomad.genomes.r2.0.2.sites
-hgmd_vcf	/work/gad/shared/pipeline/hg19/HGMD/HGMD_PRO_2017.2_hg19.vcf
-regulatoryfeatures	/work/gad/shared/pipeline/hg19/ensembl_regulation/regulatory_features.bed
-motiffeatures	/work/gad/shared/pipeline/hg19/ensembl_regulation/motif_features.bed
-encodednase	/work/gad/shared/pipeline/hg19/Encode/wgEncodeRegDnaseClusteredV3.bed
-encodetfbs	/work/gad/shared/pipeline/hg19/Encode/wgEncodeRegTfbsClusteredV3.bed
-linsight	/work/gad/shared/pipeline/hg19/LINSIGHT
-fantom	/work/gad/shared/pipeline/hg19/FANTOM/fantom_cage_peak.bed
-isgenic	/work/gad/shared/pipeline/hg19/FANTOM/isGenic.bed
-genelists	/work/gad/shared/pipeline/hg19/gene_lists/
-vtbase	/work/gad/shared/bin/vt

annotate_variants_pharmAnnot.sh

-#!/bin/ksh
-
-### GAD PIPELINE ###
-## annotate_variants_snpeff.sh
-## Version : 1.0
-## Description : This script allows user to launch SnpEff and SNpSift for basic variant annotation, frequency annotation and score annotation
-## Usage : qsub -pe smp <nb thread> -v INPUTFILE=<raw/vcf/file>,OUTPUTFILE=</path/to/the/output/vcf/file>,PHARMGKB=<ref/file/pharmgkb>,[NOCHECK=yes|no],[LOGFILE=/path/to/the/log/file],[CONFIGFILE=/path/to/the/config/file] annotate_variants_pharmAnnot.sh
-## Output : .vcf file containing annotations
-## Requirements : jdk 1.8.0
-
-## Author : Simon.Verdez@u-bourgogne.fr
-## Creation Date : 20180727
-## last revision date : 20180727
-## Known bugs : None
-
-#$ -q batch
-#$ -V
-
-
-
-# Log file path option
-if [ -z ${LOGFILE} ]
-then
-    LOGFILE=annotate_variants_snpeff.$(date +"%F_%H-%M-%S").log
-fi
-
-# Config file path option
-if [ -z ${CONFIGFILE} ]
-then
-    CONFIGFILE=analysis_config.tsv
-fi
-
-# Logging
-exec 1>> $LOGFILE 2>&1
-echo "$(date +"%F_%H-%M-%S"): START"
-
-# Check if config file exist
-if [ ! -f $CONFIGFILE ]
-then
-    echo "Config file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch annotate_variants_snpeff.failed
-    exit 1
-fi
-
-# Check if input file exist
-if [ ! -f $INPUTFILE ]
-then
-    echo "Input file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch annotate_variants_snpeff.failed
-    exit 1
-fi
-
-if [ ! -f $PHARMGKB ]
-then
-    echo "ref pharmgkb file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch annotate_variants_snpeff.failed
-    exit 1
-fi
-
-# Check if output file is specified
-if [ -z $OUTPUTFILE ]
-then
-    echo "Output file is not specified"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch annotate_variants_snpeff.failed
-    exit 1
-fi
-
-JAVA=$(grep "javacmd" $CONFIGFILE | awk '{print $2}')
-PATHSCRIPT=$(grep "pipelinebase" $CONFIGFILE | awk '{print $2}')
-SNPEFF=$(grep "snpeffbase" $CONFIGFILE | awk '{print $2}')
-
-# Launch Snpeff and SnpSift command and check exit code
-echo "Command: $JAVA -Xmx4g -jar $SNPEFF/SnpSift.jar Annotate $PHARMGKB $INPUTFILE > $OUTPUTFILE"
-bash -o pipefail  -c "$JAVA -Xmx4g -jar $SNPEFF/SnpSift.jar Annotate $PHARMGKB $INPUTFILE > $OUTPUTFILE"
-
-snpeff_exitcode=$?
-echo "snpeff exit code : $snpeff_exitcode"
-if [ $snpeff_exitcode != 0 ]
-then
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch annotate_variants_Annot.failed
-    exit 1
-fi
-
-if [ -z ${NOCHECK} ] || [ ${NOCHECK} == "no" ]
-then
-    chr=`tail -1 $OUTPUTFILE | cut -f1`
-    if [ $chr != "chrX" ] && [ $chr != "chrY" ] && [ $chr != "X" ] && [ $chr != "Y" ]
-    then
-        echo "vcf file does not seem complete"
-        echo "$(date +"%F_%H-%M-%S"): END"
-        touch annotate_variants_snpeff.failed
-        exit 1
-    fi
-fi
-
-
-echo "$(date +"%F_%H-%M-%S"): END"

haplo_scan.sh

-#!/bin/bash
-
-###GAD PIPELINE ###
-## haplo_scan.sh
-## Version : 1.0.0
-## Description : This scprit tke a bam and return a file text with HLA type
-## Usage : qsub -v BAM=<path to the bam>,SORTIE=<path to outdir>,GeneList=<path to gene list>,[LOGFILE=/path/to/the/log/file] haplo_scan.sh
-## Output : file text
-## Requirements : HLAscan
-
-## Author : Simon.Verdez@etu.u-bourgogne.fr
-## Creation Date : 20180425
-## last revision date : 20180425
-## Known bugs : None
-
-#$ -N hlascan
-#$ -q batch
-#$ -pe smp 2
-#$ -V
-
-# Log file path option
-if [ -z ${LOGFILE} ]
-then
-    LOGFILE=haplo_scan.$(date +"%F_%H-%M-%S").log
-fi
-
-# Logging
-exec 1>> $LOGFILE 2>&1
-echo "$(date +"%F_%H-%M-%S"): START"
-
-# Check if input file exist
-if [ ! -f $BAM ]
-then
-    echo "Bam file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch haplo_scan.failed
-    exit 1
-fi
-
-# Check if gene file exist
-if [ ! -f $GeneList ]
-then
-    echo "Gene file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch haplo_scan.failed
-    exit 1
-fi
-
-
-# Check if output file is specified
-if [ -z $SORTIE ]
-then
-    echo "SORTIE file is not specified"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch haplo_scan.failed
-    exit 1
-fi
-
-SAMPLE=`basename ${BAM} | cut -d . -f1`
-RES=${SORTIE}
-GL=/work/gad/shared/bin/HLAscan_v1.0/hla-ref-5gene/gene_list
-
-#Launch haplo_scan
-/bin/python2.7 /work/gad/shared/bin/HLAscan_v1.0/hla-paper/haplo_scan_v4.0-sv.py $BAM $GL $RES
-
-hla_exitcode=$?
-echo "hla_scan exit code : $hla_exitcode"
-if [ $hla_exitcode != 0 ]
-then
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch hla_scan.failed
-    exit 1
-fi
-
-echo "$(date +"%F_%H-%M-%S"): END"

merge_GATK.sh

-#!/bin/ksh
-
-### PharmAnnot PIPELINE ###
-## merge_GATK.sh
-## Version : 1.0.0
-## Description : This script merge two vcf file
-## Usage : qsub -pe smp <nb thread> -v INPUTFILE1=</path/to/the/input/vcf/file>,INPUTFILE2=</path/to/the/input/vcf/file>,REF=</path/to/the/ref/file>,OUTPUTFILE=</path/to/the/output/vcf/file>,[LOGFILE=/path/to/the/log/file],[CONFIGFILE=/path/to/the/config/file] merge_GATK.sh
-## Output : .vcf file containing annotations
-## Requirements : jdk 1.8.0
-
-## Author : simon.verdez@chu-dijon.fr
-## Creation Date : 20180702
-## last revision date : 20180702
-## Known bugs : None
-
-#$ -q batch
-#$ -V
-
-
-
-# Log file path option
-if [ -z ${LOGFILE} ]
-then
-    LOGFILE=merge_GATK.$(date +"%F_%H-%M-%S").log
-fi
-
-# Config file path option
-if [ -z ${CONFIGFILE} ]
-then
-    CONFIGFILE=analysis_config.tsv
-fi
-
-# Logging
-exec 1>> $LOGFILE 2>&1
-echo "$(date +"%F_%H-%M-%S"): START"
-
-# Check if config file exist
-if [ ! -f $CONFIGFILE ]
-then
-    echo "Config file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch merge_GATK.failed
-    exit 1
-fi
-
-# Check if input1 file exist
-if [ ! -f $INPUTFILE1 ]
-then
-    echo "Input1 file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch merge_GATK.failed
-    exit 1
-fi
-
-# Check if input2 file exist
-if [ ! -f $INPUTFILE2 ]
-then
-    echo "Input2 file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch merge_GATK.failed
-    exit 1
-fi
-
-# Check if ref file exist
-if [ ! -f $REF ]
-then
-    echo "ref file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch merge_GATK.failed
-    exit 1
-fi
-
-# Check if output file is specified
-if [ -z $OUTPUTFILE ]
-then
-    echo "Output file is not specified"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch merge_GATK.failed
-    exit 1
-fi
-
-#JAVA=$(grep "javacmd" $CONFIGFILE | awk '{print $2}')
-module load java64/1.8.0_162
-PATHSCRIPT=$(grep "pipelinebase" $CONFIGFILE | awk '{print $2}')
-#GATK=$(grep "GATKbase" $CONFIGFILE | awk '{print $2}')
-
-echo "command : $JAVA -jar /work/gad/shared/bin/GATK_3.7/GenomeAnalysisTK.jar -T CombineVariants -R $REF --variant $INPUTFILE1 --variant $INPUTFILE2 -genotypeMergeOptions UNIQUIFY"
-java -jar /work/gad/shared/bin/GATK_3.7/GenomeAnalysisTK.jar -T CombineVariants -R $REF --variant $INPUTFILE1 --variant $INPUTFILE2 -o $OUTPUTFILE -genotypeMergeOptions UNIQUIFY
-
-genotypeMerge_exitcode=$?
-echo "GenotypeMerge exit code : $genotypeMerge_exitcode"
-if [ $genotypeMerge_exitcode != 0 ]
-then
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch merge.failed
-    exit 1
-fi
-
-echo "$(date +"%F_%H-%M-%S"): END"

pharmconfig_epilepsie.tsv

-pipelinebase    /work/gad/shared/pipeline/pharmacogen_test/pharmAnnot
-HLAlist	/work/gad/shared/analyse/test_HLA/HLAscan_v1.0/hla-ref-5gene/gene_list
-pharmagkbase	/work/gad/sv347413/epilepsie/Pipeline/pharmgkb_v2.vcf
-pharmagktab	/work/gad/sv347413/epilepsie/Pipeline/tableau_pharmgkb.tsv
-omim	/work/gad/sv347413/epilepsie/Pipeline/tableau_OMIM.tsv
-header	/work/gad/sv347413/epilepsie/Pipeline/header_CNV.vcf
-reference	/work/gad/shared/pipeline/hg19/index/hg19_essential.fa

pharmconfig_oncologie.tsv

-pipelinebase	/work/gad/shared/pipeline/pharmacogen_test/pharmAnnot	
-HLAlist	/work/gad/shared/analyse/test_HLA/HLAscan_v1.0/hla-ref-5gene/gene_list
-pharmagkbase	/work/gad/sv347413/oncologie/pharmgkb_oncologie_v4.vcf
-pharmagktab	/work/gad/sv347413/oncologie/tableau_oncologie_v2.tsv
-omim	/work/gad/sv347413/oncologie/tableau_OMIM_oncologie.tsv
-header	/work/gad/sv347413/epilepsie/Pipeline/header_CNV.vcf
-reference	/work/gad/shared/pipeline/hg19/index/hg19_essential.fa

tsv2vcf.py

-#!/usr/bin/python
-
-### PharmAnnot PIPELINE ###
-## tsv2vcf.py
-## Version : 1.1.0
-## Description : Conversion a tsv file in vcf file.
-## Usage : python tsv2vcf.py -i <input/tsv/file> -p <input/tsv/file> -m<input/tsv/file> -r <reference/bam/fie> -o <output/vcf/file> -e <log/file>
-## Output : vcf file
-## Requirements : python 2.7+
-
-## Author : Simon.Verdez@chu-dijon.fr
-## Creation Date : 20180709
-## last revision date : 20180731
-## Known bugs : None
-
-import os
-import sys
-import vcf
-import csv
-from VCF_tools import *
-import subprocess
-from operator import *
-import getopt
-import logging
-
-#Options
-try:
-    opts, args = getopt.getopt(sys.argv[1:], 'i:p:m:r:o:e:')
-    for opt, arg in opts:
-        if opt in ("-i"):
-            tsvfile = arg
-        if opt in ("-p"):
-            pharmgkb = arg
-        if opt in ("-m"):
-            OMIM = arg
-        if opt in ("-r"):
-            REFERENCE = arg
-        elif opt in ("-o"):
-            out_vcf = arg
-        elif opt in ("-e"):
-            logfile = arg
-except getopt.GetoptError:
-    print 'usage : '
-    sys.exit(1)
-
-# Logging
-logging.basicConfig(filename =  '%s' % (logfile), filemode = 'a', level = logging.INFO, format = '%(asctime)s %(levelname)s - %(message)s')
-logging.info('start')
-
-# Manage options
-if not vars().has_key('tsvfile'):
-    logging.exception('No input file given')
-    sys.exit(1)
-if not vars().has_key('pharmgkb'):
-    logging.exception('No pharmgkb database given')
-    sys.exit(1)
-if not vars().has_key('OMIM'):
-    logging.exception('No OMIM database given')
-    sys.exit(1)
-if not vars().has_key('REFERENCE'):
-    logging.exception('No REFERENCE bam given')
-    sys.exit(1)
-
-# Check files
-try:
-	f = open(tsvfile, 'r')
-	f.close()
-except IOError:
-    logging.exception('Input file does not exist')
-    sys.exit(1)
-try:
-	f = open(pharmgkb, 'r')
-	f.close()
-except IOError:
-    logging.exception('Clinvar file does not exist')
-    sys.exit(1)
-try:
-	f = open(OMIM, 'r')
-	f.close()
-except IOError:
-    logging.exception('Hgmd file does not exist')
-    sys.exit(1)
-try:
-	f = open(REFERENCE, 'r')
-	f.close()
-except IOError:
-    logging.exception('reference bam file does not exist')
-    sys.exit(1)
-
-
-"""Liste contenant les genes d'interets"""
-ListeG = []
-
-"""recuperation des genes dans le fichier"""
-with open(pharmgkb) as pharmfile:
-    reader = csv.DictReader(pharmfile, dialect='excel-tab')
-    for row in reader:
-        if row['gene'] != "":
-            if row['gene'] not in ListeG:
-                ListeG.append(row['gene'])
-with open(OMIM) as OMIMfile:
-    reader = csv.DictReader(OMIMfile, dialect='excel-tab')
-    for row in reader:
-        if row['GENE'] != "":
-            if row['GENE'] not in ListeG:
-                ListeG.append(row['GENE'])
-#print ListeG
-
-"""ecriture des lignes CNV dans le vcf"""
-
-ListeVCF=[]
-
-for gene in ListeG:
-    with open(tsvfile) as file:
-        reader = csv.DictReader(file, dialect='excel-tab')
-        for row in reader:
-            if gene in row['GeneList'] and gene != "":
-                line_vcf = VCF_CNV()
-                line_vcf.CHROM = row["#CHR"]
-                line_vcf.POS = row["START"]
-                p = subprocess.Popen(["samtools", 'faidx',REFERENCE, row["#CHR"]+":"+row["START"]+"-"+row["START"]], stdout = subprocess.PIPE)
-                line_vcf.REF = p.stdout.readlines()[1].strip("\n")
-                line_vcf.ALT = "<"+row["CNV"]+">"
-                line_vcf.QUAL = "6"
-                line_vcf.SVTYPE = row["CNV"]
-                line_vcf.END = row["END"]
-                if row["CNV"] == "DEL":
-                    line_vcf.SVLEN = "-"+row["CNVLength"]
-                else :
-                    line_vcf.SVLEN =row["CNVLength"]
-                line_vcf.GENE = str(gene)
-                ListeVCF.append(line_vcf)
-
-ListeVCF = sorted(ListeVCF,key=attrgetter('POS'))
-
-header = create_header()
-
-with open (out_vcf,'w') as vcf_out:
-    vcf_out.write(header)
-
-for line in ListeVCF:
-    with open (out_vcf,'a') as vcf_out:
-        vcf_out.write(repr(line)+"\n")

wrapper_create_html.sh

-#!/bin/ksh
-
-### GAD PIPELINE ###
-## wrapper_create_html.sh
-## Version : 1.0.0
-## Description : a wrapper for qsubing create_html.py script
-## Usage : qsub -pe smp <nb thread> -v VCF_SNP=</path/to/the/input/vcf/file>,VCF_CNV=</path/to/the/input/vcf/file>,REPORTFILE=<path/to/the/HLAscan/report>,BAMFILE=</path/to/the/bam>,TSVFILE=</path/to/the/tsv>,OUTPUTFILE=</path/to/the/output/vcf/file>,[LOGFILE=/path/to/the/log/file],[CONFIGFILE=/path/to/the/config/file] wrapper_create_html.sh
-## Output : create_html.py output
-## Requirements : Recquire script create_html.py and VcfTools
-
-## Author : Simon.Verdez@u-bourgogne.fr
-## Creation Date : 20180802
-## last revision date : 20180802
-## Known bugs : None
-
-#$ -q batch
-#$ -V
-
-
-# Log file path option
-if [ -z ${LOGFILE} ]
-then
-    LOGFILE=annotate_variants.$(date +"%F_%H-%M-%S").log
-fi
-
-# Config file path option
-if [ -z ${CONFIGFILE} ]
-then
-    CONFIGFILE=analysis_config.tsv
-fi
-
-# Logging
-exec 1>> $LOGFILE 2>&1
-echo "$(date +"%F_%H-%M-%S"): START"
-
-# Check if config file exist
-if [ ! -f $VCF_SNP ]
-then
-    echo "Vcf SNP file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch create_html.failed
-    exit 1
-fi
-
-if [ ! -f $VCF_CNV ]
-then
-    echo "Vcf CNV file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch create_html.failed
-    exit 1
-fi
-
-if [ ! -f $REPORTFILE ]
-then
-    echo "Report HLAscan file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch create_html.failed
-    exit 1
-fi
-
-if [ ! -f $BAMFILE ]
-then
-    echo "BAM file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch create_html.failed
-    exit 1
-fi
-
-if [ ! -f $TSVFILE ]
-then
-    echo "TSV file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch create_html.failed
-    exit 1
-fi
-
-# Check if output file is specified
-if [ -z $OUTPUTFILE ]
-then
-    echo "Output file is not specified"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch create_html.failed
-    exit 1
-fi
-
-PYTHONBIN=`grep pythonbin $CONFIGFILE | cut -f2`
-PIPELINEBASE=`grep pipelinebase $CONFIGFILE | cut -f2`
-
-# Launch python script command and check exit code
-echo "command : $PIPELINEBASE/create_html.py -v $VCF_SNP -c $VCF_CNV -h $REPORTFILE -b $BAMFILE -t $TSVFILE -o $OUTPUTFILE -e $LOGFILE"
-$PYTHONBIN $PIPELINEBASE/create_html.py -v $VCF_SNP -c $VCF_CNV -h $REPORTFILE -b $BAMFILE -t $TSVFILE -o $OUTPUTFILE -e $LOGFILE
-create_html_exitcode=$?
-echo "create_html exit code : $annotate_variants_exitcode"
-if [ $creaete_html_exitcode != 0 ]
-then
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch create_html.failed
-    exit 1
-fi
-
-echo "$(date +"%F_%H-%M-%S"): END"

wrapper_tsv2vcf.sh

-#!/bin/ksh
-
-### GAD PIPELINE ###
-## wrapper_tsv2vcf.sh
-## Version : 1.0.0
-## Description : a wrapper for qsubing tsv2vcf.py script
-## Usage : qsub -pe smp <nb thread> -v INPUTFILE=</path/to/the/input/tsv/file>,PHARMGKB=<ref/file/pharmgkb>,OMIM=<ref/file/OMIM>,REF=<ref/bam/file>,OUTPUTFILE=</path/to/the/output/vcf/file>,[LOGFILE=/path/to/the/log/file],[CONFIGFILE=/path/to/the/config/file] wrapper_tsv2vcf.sh
-## Output : annotate_variants.py output
-## Requirements : Recquire script tsv2vcf.py and VcfTools
-
-## Author : Simon.Verdez@u-bourgogne.fr
-## Creation Date : 20180702
-## last revision date : 20180702
-## Known bugs : None
-
-#$ -q batch
-#$ -V
-
- Log file path option
-if [ -z ${LOGFILE} ]
-then
-    LOGFILE=annotate_variants.$(date +"%F_%H-%M-%S").log
-fi
-
-# Config file path option
-if [ -z ${CONFIGFILE} ]
-then
-    CONFIGFILE=analysis_config.tsv
-fi
-
-# Logging
-exec 1>> $LOGFILE 2>&1
-echo "$(date +"%F_%H-%M-%S"): START"
-
-# Check if config file exist
-if [ ! -f $CONFIGFILE ]
-then
-    echo "Config file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch tsv2vcf.failed
-    exit 1
-fi
-
-# Check if input file exist
-if [ ! -f $INPUTFILE ]
-then
-    echo "Input file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch tsv2vcf.failed
-    exit 1
-fi
-
-if [ ! -f $PHARMGKB ]
-then
-    echo "PHARMGKB reference file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch tsv2vcf.failed
-    exit 1
-fi
-
-if [ ! -f $OMIM ]
-then
-    echo "OMIM reference file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch tsv2vcf.failed
-    exit 1
-fi
-
-if [ ! -f $REF ]
-then
-    echo "reference bam file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch tsv2vcf.failed
-    exit 1
-fi
-
-# Check if output file is specified
-if [ -z $OUTPUTFILE ]
-then
-    echo "Output file is not specified"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch tsv2vcf.failed
-    exit 1
-fi
-
-PYTHONBIN=`grep pythonbin $CONFIGFILE | cut -f2`
-PIPELINEBASE=`grep pipelinebase $CONFIGFILE | cut -f2`
-
-# Launch python script command and check exit code
-echo "command : $PIPELINEBASE/tsv2vcf.py -i $INPUTFILE -p $PHARMGKB -m $OMIM -r $REF -o $OUTPUTFILE -e $LOGFILE"
-$PYTHONBIN $PIPELINEBASE/tsv2vcf.py -i $INPUTFILE -p $PHARMGKB -m $OMIM -r $REF -o $OUTPUTFILE -e $LOGFILE
-tsv2vcf_exitcode=$?
-echo "tsv2vcf exit code : $tsv2vcf_exitcode"
-if [ $tsv2vcf_exitcode != 0 ]
-then
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch tsv2vcf.failed
-    exit 1
-fi
-
-echo "$(date +"%F_%H-%M-%S"): END"