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gad-public
pharmAnnot
Commits
0208c5db
Commit
0208c5db
authored
Aug 10, 2018
by
Simon Verdez
Browse files
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pipeline epilepsie
parent
99b711dc
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7 changed files
with
32 additions
and
9 deletions
+32
-9
Dup_Data.sh
Dup_Data.sh
+17
-0
Master.sh
Master.sh
+8
-4
VCF_tools.py
VCF_tools.py
+1
-0
VCF_tools.pyc
VCF_tools.pyc
+0
-0
create_html_v2.py
create_html_v2.py
+0
-0
haplo_scan.sh
haplo_scan.sh
+2
-2
merge_GATK.sh
merge_GATK.sh
+4
-3
No files found.
Dup_Data.sh
0 → 100755
View file @
0208c5db
#!/bin/bash
if
[
!
-e
/work/gad/sv347413/epilepsie/vcf_tmp/
$i
*
.vcf
]
then
for
i
in
$(
cat
/work/gad/sv347413/HLAscan/liste_patients_epileptiques.txt
)
do
cp
/work/gad/shared/vcf/individu/
$i
/
*
.raw.vcf /work/gad/sv347413/epilepsie/vcf_tmp/.
done
fi
if
[
!
-e
/work/gad/sv347413/epilepsie/tsv_tmp/
$i
*
.tsv
]
then
for
i
in
$(
cat
/work/gad/sv347413/HLAscan/liste_patients_epileptiques.txt
)
do
cp
/work/gad/shared/vcf/individu/
$i
/
*
.cnv.annot.tsv /work/gad/sv347413/epilepsie/tsv_tmp/.
done
fi
Master.sh
View file @
0208c5db
...
@@ -64,7 +64,6 @@ REF=`grep "reference" $PHARMCONFIG | cut -f2`
...
@@ -64,7 +64,6 @@ REF=`grep "reference" $PHARMCONFIG | cut -f2`
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/
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
export
PYTHONPATH
# Sample list
# Sample list
samples
=
`
find
-L
$ANALYSISDIR
/
-maxdepth
1
-mindepth
1
-type
d | xargs
-l
basename
`
samples
=
`
find
-L
$ANALYSISDIR
/
-maxdepth
1
-mindepth
1
-type
d | xargs
-l
basename
`
...
@@ -75,16 +74,18 @@ then
...
@@ -75,16 +74,18 @@ then
fi
fi
find
-L
$ANALYSISDIR
/
-maxdepth
1
-mindepth
1
-type
d | xargs
-l
basename
>>
$ANALYSISDIR
/batch.list
find
-L
$ANALYSISDIR
/
-maxdepth
1
-mindepth
1
-type
d | xargs
-l
basename
>>
$ANALYSISDIR
/batch.list
HLAscan:
# HLA genotyping
# HLA genotyping
echo
"### Execute HLAscan ###"
echo
"### Execute HLAscan ###"
echo
"Start :
$(
date
+
"%F_%H-%M-%S"
)
"
echo
"Start :
$(
date
+
"%F_%H-%M-%S"
)
"
for
currentSample
in
$samples
for
currentSample
in
$samples
do
do
echo
"Command : qsub -pe smp
2
-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"
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
-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
qsub
-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
done
echo
"End :
$(
date
+
"%F_%H-%M-%S"
)
"
echo
"End :
$(
date
+
"%F_%H-%M-%S"
)
"
varcallSNP:
# Variant calling first step
# Variant calling first step
echo
"### Variant calling SNP first step ###"
echo
"### Variant calling SNP first step ###"
echo
"Start :
$(
date
+
"%F_%H-%M-%S"
)
"
echo
"Start :
$(
date
+
"%F_%H-%M-%S"
)
"
...
@@ -95,6 +96,7 @@ do
...
@@ -95,6 +96,7 @@ do
done
done
echo
"End :
$(
date
+
"%F_%H-%M-%S"
)
"
echo
"End :
$(
date
+
"%F_%H-%M-%S"
)
"
varcallCNV:
# Variant calling second step
# Variant calling second step
echo
"### Variant calling CNV second step ###"
echo
"### Variant calling CNV second step ###"
echo
"Start :
$(
date
+
"%F_%H-%M-%S"
)
"
echo
"Start :
$(
date
+
"%F_%H-%M-%S"
)
"
...
@@ -106,22 +108,24 @@ do
...
@@ -106,22 +108,24 @@ do
done
done
echo
"End :
$(
date
+
"%F_%H-%M-%S"
)
"
echo
"End :
$(
date
+
"%F_%H-%M-%S"
)
"
createHTML:
# Generate a HTML report_vcf
# Generate a HTML report_vcf
echo
"### Generate HTML report ###"
echo
"### Generate HTML report ###"
echo
"Start :
$(
date
+
"%F_%H-%M-%S"
)
"
echo
"Start :
$(
date
+
"%F_%H-%M-%S"
)
"
for
currentSample
in
$samples
for
currentSample
in
$samples
do
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"
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
-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
-pe
smp 1
-hold_jid
varcallCNV_
${
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
done
echo
"End :
$(
date
+
"%F_%H-%M-%S"
)
"
echo
"End :
$(
date
+
"%F_%H-%M-%S"
)
"
MergeVCF:
#merge vcf fies
#merge vcf fies
echo
"### Merge VCF files"
echo
"### Merge VCF files"
echo
"Start :
$(
date
+
"%F_%H-%M-%S"
)
"
echo
"Start :
$(
date
+
"%F_%H-%M-%S"
)
"
for
currentSample
in
$samples
for
currentSample
in
$samples
do
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"
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
-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
.merge.vcf,LOGFILE
=
$ANALYSISDIR
/
$currentSample
/logs/merge_file.
$logbasename
.log,CONFIGFILE
=
$CONFIGFILE
$PIPELINEBASE
/merge_GATK.sh
qsub
-pe
smp 1
-
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
done
echo
"End :
$(
date
+
"%F_%H-%M-%S"
)
"
echo
"End :
$(
date
+
"%F_%H-%M-%S"
)
"
VCF_tools.py
View file @
0208c5db
...
@@ -74,5 +74,6 @@ def create_header():
...
@@ -74,5 +74,6 @@ def create_header():
##contig=<ID=chr22,length=51304566>
##contig=<ID=chr22,length=51304566>
##contig=<ID=chrX,length=155270560>
##contig=<ID=chrX,length=155270560>
##contig=<ID=chrY,length=59373566>
##contig=<ID=chrY,length=59373566>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT dijex
"""
"""
return
header
return
header
VCF_tools.pyc
View file @
0208c5db
No preview for this file type
create_html_v2.py
deleted
100755 → 0
View file @
99b711dc
This diff is collapsed.
Click to expand it.
haplo_scan.sh
View file @
0208c5db
...
@@ -15,7 +15,7 @@
...
@@ -15,7 +15,7 @@
#$ -N hlascan
#$ -N hlascan
#$ -q batch
#$ -q batch
#$ -pe smp
1
#$ -pe smp
2
#$ -V
#$ -V
# Log file path option
# Log file path option
...
@@ -66,7 +66,7 @@ fi
...
@@ -66,7 +66,7 @@ fi
SAMPLE
=
`
basename
${
BAM
}
|
cut
-d
.
-f1
`
SAMPLE
=
`
basename
${
BAM
}
|
cut
-d
.
-f1
`
RES
=
${
SORTIE
}
RES
=
${
SORTIE
}
GL
=
/work/gad/shared/
analyse/test_HLA
/HLAscan_v1.0/hla-ref-5gene/gene_list
GL
=
/work/gad/shared/
bin
/HLAscan_v1.0/hla-ref-5gene/gene_list
#Launch haplo_scan
#Launch haplo_scan
/work/gad/shared/bin/miniconda2/bin/python2.7 /work/gad/shared/bin/HLAscan_v1.0/hla-paper/haplo_scan_v4.0-sv.py
$BAM
$GL
$RES
/work/gad/shared/bin/miniconda2/bin/python2.7 /work/gad/shared/bin/HLAscan_v1.0/hla-paper/haplo_scan_v4.0-sv.py
$BAM
$GL
$RES
...
...
merge_GATK.sh
View file @
0208c5db
...
@@ -79,12 +79,13 @@ then
...
@@ -79,12 +79,13 @@ then
exit
1
exit
1
fi
fi
JAVA
=
$(
grep
"javacmd"
$CONFIGFILE
|
awk
'{print $2}'
)
#JAVA=$(grep "javacmd" $CONFIGFILE | awk '{print $2}')
module load java64/1.8.0_162
PATHSCRIPT
=
$(
grep
"pipelinebase"
$CONFIGFILE
|
awk
'{print $2}'
)
PATHSCRIPT
=
$(
grep
"pipelinebase"
$CONFIGFILE
|
awk
'{print $2}'
)
#GATK=$(grep "GATKbase" $CONFIGFILE | awk '{print $2}')
#GATK=$(grep "GATKbase" $CONFIGFILE | awk '{print $2}')
echo
"command :
$JAVA
-jar /work/gad/shared/bin/GATK_3.
8/GenomeAnalysisTK.jar -T CombineVariants -R
$REF
--variant
$INPUTFILE1
--variant
$INPUTFILE2
-o merge.vcf
-genotypeMergeOptions UNIQUIFY"
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_3.8/GenomeAnalysisTK.jar
-T
CombineVariants
-R
$REF
--variant
$INPUTFILE2
--variant
$INPUTFILE2
-genotypeMergeOptions
UNIQUIFY
>
$OUTPUTFILE
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
=
$?
genotypeMerge_exitcode
=
$?
echo
"GenotypeMerge exit code :
$genotypeMerge_exitcode
"
echo
"GenotypeMerge exit code :
$genotypeMerge_exitcode
"
...
...
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