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process_scripts
Commits
dd506bbc
Commit
dd506bbc
authored
4 years ago
by
Brandi Cantarel
Browse files
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updates variant calling isdocker; module load
parent
ac7a88b4
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Changes
3
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3 changed files
variants/germline_vc.sh
+32
-15
32 additions, 15 deletions
variants/germline_vc.sh
variants/somatic_vc.sh
+33
-14
33 additions, 14 deletions
variants/somatic_vc.sh
variants/svcalling.sh
+9
-4
9 additions, 4 deletions
variants/svcalling.sh
with
74 additions
and
33 deletions
variants/germline_vc.sh
+
32
−
15
View file @
dd506bbc
...
@@ -62,9 +62,11 @@ then
...
@@ -62,9 +62,11 @@ then
interval
=
$tbed
interval
=
$tbed
fi
fi
source
/etc/profile.d/modules.sh
if
[[
-z
$isdocker
]]
module load python/2.7.x-anaconda picard/2.10.3 samtools/gcc/1.8 bcftools/gcc/1.8 bedtools/2.26.0 snpeff/4.3q vcftools/0.1.14 parallel
then
source
/etc/profile.d/modules.sh
module load python/2.7.x-anaconda picard/2.10.3 samtools/gcc/1.8 bcftools/gcc/1.8 bedtools/2.26.0 snpeff/4.3q vcftools/0.1.14 parallel
fi
for
i
in
*
.bam
;
do
for
i
in
*
.bam
;
do
if
[[
!
-f
${
i
}
.bai
]]
if
[[
!
-f
${
i
}
.bai
]]
then
then
...
@@ -81,7 +83,10 @@ then
...
@@ -81,7 +83,10 @@ then
bgzip
${
pair_id
}
.sam.vcf
bgzip
${
pair_id
}
.sam.vcf
elif
[[
$algo
==
'fb'
]]
elif
[[
$algo
==
'fb'
]]
then
then
module load freebayes/gcc/1.2.0 parallel/20150122
if
[[
-z
$isdocker
]]
then
module load freebayes/gcc/1.2.0 parallel/20150122
fi
bamlist
=
''
bamlist
=
''
for
i
in
*
.bam
;
do
for
i
in
*
.bam
;
do
bamlist
=
"
$bamlist
--bam
${
PWD
}
/
${
i
}
"
bamlist
=
"
$bamlist
--bam
${
PWD
}
/
${
i
}
"
...
@@ -92,7 +97,10 @@ then
...
@@ -92,7 +97,10 @@ then
vcf-concat fb.
*
.vcf | vcf-sort | vcf-annotate
-n
--fill-type
| bcftools norm
-c
s
-f
${
reffa
}
-w
10
-O
z
-o
${
pair_id
}
.fb.vcf.gz -
vcf-concat fb.
*
.vcf | vcf-sort | vcf-annotate
-n
--fill-type
| bcftools norm
-c
s
-f
${
reffa
}
-w
10
-O
z
-o
${
pair_id
}
.fb.vcf.gz -
elif
[[
$algo
==
'platypus'
]]
elif
[[
$algo
==
'platypus'
]]
then
then
module load platypus/gcc/0.8.1
if
[[
-z
$isdocker
]]
then
module load platypus/gcc/0.8.1
fi
bamlist
=
`
join_by ,
*
.bam
`
bamlist
=
`
join_by ,
*
.bam
`
Platypus.py callVariants
--minMapQual
=
0
--minReads
=
3
--mergeClusteredVariants
=
1
--nCPU
=
$NPROC
--bamFiles
=
${
bamlist
}
--refFile
=
${
reffa
}
--output
=
platypus.vcf
Platypus.py callVariants
--minMapQual
=
0
--minReads
=
3
--mergeClusteredVariants
=
1
--nCPU
=
$NPROC
--bamFiles
=
${
bamlist
}
--refFile
=
${
reffa
}
--output
=
platypus.vcf
vcf-sort platypus.vcf |vcf-annotate
-n
--fill-type
-n
|bgzip
>
platypus.vcf.gz
vcf-sort platypus.vcf |vcf-annotate
-n
--fill-type
-n
|bgzip
>
platypus.vcf.gz
...
@@ -107,7 +115,10 @@ then
...
@@ -107,7 +115,10 @@ then
usage
usage
fi
fi
user
=
$USER
user
=
$USER
module load gatk/4.1.4.0
if
[[
-z
$isdocker
]]
then
module load gatk/4.1.4.0
fi
gvcflist
=
''
gvcflist
=
''
for
i
in
*
.bam
;
do
for
i
in
*
.bam
;
do
prefix
=
"
${
i
%.bam
}
"
prefix
=
"
${
i
%.bam
}
"
...
@@ -123,14 +134,17 @@ then
...
@@ -123,14 +134,17 @@ then
tabix
${
pair_id
}
.gatk.vcf.gz
tabix
${
pair_id
}
.gatk.vcf.gz
elif
[
$algo
==
'mutect'
]
elif
[
$algo
==
'mutect'
]
then
then
module load gatk/4.1.4.0 parallel/20150122
if
[[
-z
$isdocker
]]
threads
=
`
expr
$NPROC
/ 2
`
then
bamlist
=
''
module load gatk/4.1.4.0 parallel/20150122
for
i
in
*
.bam
;
do
fi
bamlist+
=
"-I
${
i
}
"
threads
=
`
expr
$NPROC
/ 2
`
done
bamlist
=
''
gatk
--java-options
"-Xmx20g"
Mutect2
$ponopt
-R
${
reffa
}
${
bamlist
}
--output
${
pair_id
}
.mutect.vcf
-RF
AllowAllReadsReadFilter
--independent-mates
--tmp-dir
`
pwd
`
-L
$interval
for
i
in
*
.bam
;
do
vcf-sort
${
pair_id
}
.mutect.vcf | vcf-annotate
-n
--fill-type
| java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
-p
'(GEN[*].DP >= 10)'
| bgzip
>
${
pair_id
}
.mutect.vcf.gz
bamlist+
=
"-I
${
i
}
"
done
gatk
--java-options
"-Xmx20g"
Mutect2
$ponopt
-R
${
reffa
}
${
bamlist
}
--output
${
pair_id
}
.mutect.vcf
-RF
AllowAllReadsReadFilter
--independent-mates
--tmp-dir
`
pwd
`
-L
$interval
vcf-sort
${
pair_id
}
.mutect.vcf | vcf-annotate
-n
--fill-type
| java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
-p
'(GEN[*].DP >= 10)'
| bgzip
>
${
pair_id
}
.mutect.vcf.gz
elif
[[
$algo
==
'strelka2'
]]
elif
[[
$algo
==
'strelka2'
]]
then
then
opt
=
''
opt
=
''
...
@@ -152,7 +166,10 @@ then
...
@@ -152,7 +166,10 @@ then
else
else
mode
=
"--exome"
mode
=
"--exome"
fi
fi
module load strelka/2.9.10 manta/1.3.1
if
[[
-z
$isdocker
]]
then
module load strelka/2.9.10 manta/1.3.1
fi
mkdir
manta strelka
mkdir
manta strelka
gvcflist
=
''
gvcflist
=
''
for
i
in
*
.bam
;
do
for
i
in
*
.bam
;
do
...
...
This diff is collapsed.
Click to expand it.
variants/somatic_vc.sh
+
33
−
14
View file @
dd506bbc
...
@@ -34,8 +34,11 @@ do
...
@@ -34,8 +34,11 @@ do
esac
esac
done
done
source
/etc/profile.d/modules.sh
if
[[
-z
$isdocker
]]
module load htslib/gcc/1.8 samtools/gcc/1.8 snpeff/4.3q vcftools/0.1.14
then
source
/etc/profile.d/modules.sh
module load htslib/gcc/1.8 samtools/gcc/1.8 snpeff/4.3q vcftools/0.1.14
fi
export
PATH
=
/project/shared/bicf_workflow_ref/seqprg/bin:
$PATH
export
PATH
=
/project/shared/bicf_workflow_ref/seqprg/bin:
$PATH
shift
$((
$OPTIND
-
1
))
shift
$((
$OPTIND
-
1
))
...
@@ -83,7 +86,10 @@ fi
...
@@ -83,7 +86,10 @@ fi
if
[
$algo
==
'strelka2'
]
if
[
$algo
==
'strelka2'
]
then
then
module load strelka/2.9.10 manta/1.3.1
if
[[
-z
$isdocker
]]
then
module load strelka/2.9.10 manta/1.3.1
fi
opt
=
''
opt
=
''
if
[[
-n
$tbed
]]
if
[[
-n
$tbed
]]
then
then
...
@@ -110,7 +116,10 @@ then
...
@@ -110,7 +116,10 @@ then
vcf-concat strelka/results/variants/
*
.vcf.gz | vcf-annotate
-n
--fill-type
-n
|vcf-sort |java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
"(GEN[*].DP >= 10)"
| perl
-pe
"s/TUMOR/
${
tid
}
/g"
| perl
-pe
"s/NORMAL/
${
nid
}
/g"
|bgzip
>
${
pair_id
}
.strelka2.vcf.gz
vcf-concat strelka/results/variants/
*
.vcf.gz | vcf-annotate
-n
--fill-type
-n
|vcf-sort |java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
"(GEN[*].DP >= 10)"
| perl
-pe
"s/TUMOR/
${
tid
}
/g"
| perl
-pe
"s/NORMAL/
${
nid
}
/g"
|bgzip
>
${
pair_id
}
.strelka2.vcf.gz
elif
[
$algo
==
'virmid'
]
elif
[
$algo
==
'virmid'
]
then
then
module load virmid/1.2
if
[[
-z
$isdocker
]]
then
module load virmid/1.2
fi
cosmic
=
${
index_path
}
/cosmic.vcf.gz
cosmic
=
${
index_path
}
/cosmic.vcf.gz
if
[[
!
-f
"
${
index_path
}
/cosmic.vcf.gz"
]]
if
[[
!
-f
"
${
index_path
}
/cosmic.vcf.gz"
]]
then
then
...
@@ -120,20 +129,29 @@ then
...
@@ -120,20 +129,29 @@ then
virmid
-R
${
reffa
}
-D
${
tumor
}
-N
${
normal
}
-s
${
cosmic
}
-t
$NPROC
-M
2000
-c1
10
-c2
10
virmid
-R
${
reffa
}
-D
${
tumor
}
-N
${
normal
}
-s
${
cosmic
}
-t
$NPROC
-M
2000
-c1
10
-c2
10
perl
$baseDir
/addgt_virmid.pl
${
tumor
}
.virmid.som.passed.vcf
perl
$baseDir
/addgt_virmid.pl
${
tumor
}
.virmid.som.passed.vcf
perl
$baseDir
/addgt_virmid.pl
${
tumor
}
.virmid.loh.passed.vcf
perl
$baseDir
/addgt_virmid.pl
${
tumor
}
.virmid.loh.passed.vcf
module
rm
java/oracle/jdk1.7.0_51
if
[[
-z
$isdocker
]]
module load snpeff/4.3q
then
module
rm
java/oracle/jdk1.7.0_51
module load snpeff/4.3q
fi
vcf-concat
*
gt.vcf | vcf-sort | vcf-annotate
-n
--fill-type
-n
| java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
'((NDP >= 10) & (DDP >= 10))'
| perl
-pe
"s/TUMOR/
${
tid
}
/g"
| perl
-pe
"s/NORMAL/
${
nid
}
/g"
| bgzip
>
${
pair_id
}
.virmid.vcf.gz
vcf-concat
*
gt.vcf | vcf-sort | vcf-annotate
-n
--fill-type
-n
| java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
'((NDP >= 10) & (DDP >= 10))'
| perl
-pe
"s/TUMOR/
${
tid
}
/g"
| perl
-pe
"s/NORMAL/
${
nid
}
/g"
| bgzip
>
${
pair_id
}
.virmid.vcf.gz
elif
[
$algo
==
'mutect'
]
elif
[
$algo
==
'mutect'
]
then
then
module load gatk/4.1.4.0 parallel/20150122
if
[[
-z
$isdocker
]]
then
module load gatk/4.1.4.0 parallel/20150122
fi
threads
=
`
expr
$NPROC
/ 2
`
threads
=
`
expr
$NPROC
/ 2
`
gatk
--java-options
"-Xmx20g"
Mutect2
$ponopt
--independent-mates
-RF
AllowAllReadsReadFilter
-R
${
reffa
}
-I
${
tumor
}
-tumor
${
tid
}
-I
${
normal
}
-normal
${
nid
}
--output
${
tid
}
.mutect.vcf
-L
$interval
gatk
--java-options
"-Xmx20g"
Mutect2
$ponopt
--independent-mates
-RF
AllowAllReadsReadFilter
-R
${
reffa
}
-I
${
tumor
}
-tumor
${
tid
}
-I
${
normal
}
-normal
${
nid
}
--output
${
tid
}
.mutect.vcf
-L
$interval
vcf-concat
${
tid
}
.mutect.
*
vcf | vcf-sort | vcf-annotate
-n
--fill-type
| java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
-p
'(GEN[*].DP >= 10)'
| bgzip
>
${
pair_id
}
.mutect.vcf.gz
vcf-concat
${
tid
}
.mutect.
*
vcf | vcf-sort | vcf-annotate
-n
--fill-type
| java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
-p
'(GEN[*].DP >= 10)'
| bgzip
>
${
pair_id
}
.mutect.vcf.gz
elif
[
$algo
==
'varscan'
]
elif
[
$algo
==
'varscan'
]
then
then
module load bcftools/gcc/1.8 VarScan/2.4.2
if
[[
-z
$isdocker
]]
module
rm
java/oracle/jdk1.7.0_51
then
module load snpeff/4.3q
module load bcftools/gcc/1.8 VarScan/2.4.2
module
rm
java/oracle/jdk1.7.0_51
module load snpeff/4.3q
fi
samtools mpileup
-C
50
-f
${
reffa
}
$tumor
>
t.mpileup
samtools mpileup
-C
50
-f
${
reffa
}
$tumor
>
t.mpileup
samtools mpileup
-C
50
-f
${
reffa
}
$normal
>
n.mpileup
samtools mpileup
-C
50
-f
${
reffa
}
$normal
>
n.mpileup
VarScan somatic n.mpileup t.mpileup vscan
--output-vcf
1
VarScan somatic n.mpileup t.mpileup vscan
--output-vcf
1
...
@@ -141,13 +159,14 @@ then
...
@@ -141,13 +159,14 @@ then
vcf-concat vscan
*
.vcf | vcf-sort | vcf-annotate
-n
--fill-type
-n
| java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
'((exists SOMATIC) & (GEN[*].DP >= 10))'
| perl
-pe
"s/TUMOR/
${
tid
}
/"
| perl
-pe
"s/NORMAL/
${
nid
}
/g"
| bgzip
>
${
pair_id
}
.varscan.vcf.gz
vcf-concat vscan
*
.vcf | vcf-sort | vcf-annotate
-n
--fill-type
-n
| java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
'((exists SOMATIC) & (GEN[*].DP >= 10))'
| perl
-pe
"s/TUMOR/
${
tid
}
/"
| perl
-pe
"s/NORMAL/
${
nid
}
/g"
| bgzip
>
${
pair_id
}
.varscan.vcf.gz
elif
[
$algo
==
'shimmer'
]
elif
[
$algo
==
'shimmer'
]
then
then
module load R/3.6.1-gccmkl
if
[[
-z
$isdocker
]]
module
rm
perl/5.18.2
then
module load R/3.6.1-gccmkl
module
rm
perl/5.18.2
fi
shimmer.pl
--minqual
25
--ref
${
reffa
}
${
normal
}
${
tumor
}
--outdir
shimmer 2> shimmer.err
shimmer.pl
--minqual
25
--ref
${
reffa
}
${
normal
}
${
tumor
}
--outdir
shimmer 2> shimmer.err
perl
$baseDir
/add_readct_shimmer.pl
perl
$baseDir
/add_readct_shimmer.pl
module
rm
java/oracle/jdk1.7.0_51
module
rm
java/oracle/jdk1.7.0_51
module load snpeff/4.3q
module load snpeff/4.3q
vcf-annotate
-n
--fill-type
shimmer/somatic_diffs.readct.vcf | java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
'(GEN[*].DP >= 10)'
| perl
-pe
"s/TUMOR/
${
tid
}
/"
| perl
-pe
"s/NORMAL/
${
nid
}
/g"
| bgzip
>
${
pair_id
}
.shimmer.vcf.gz
vcf-annotate
-n
--fill-type
shimmer/somatic_diffs.readct.vcf | java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
'(GEN[*].DP >= 10)'
| perl
-pe
"s/TUMOR/
${
tid
}
/"
| perl
-pe
"s/NORMAL/
${
nid
}
/g"
| bgzip
>
${
pair_id
}
.shimmer.vcf.gz
fi
fi
This diff is collapsed.
Click to expand it.
variants/svcalling.sh
+
9
−
4
View file @
dd506bbc
...
@@ -58,9 +58,11 @@ if [[ -z $snpeffgeno ]]
...
@@ -58,9 +58,11 @@ if [[ -z $snpeffgeno ]]
then
then
snpeffgeno
=
'GRCh38.86'
snpeffgeno
=
'GRCh38.86'
fi
fi
if
[[
-z
$isdocker
]]
source
/etc/profile.d/modules.sh
then
module load htslib/gcc/1.8 samtools/gcc/1.8 bcftools/gcc/1.8 bedtools/2.26.0 snpeff/4.3q vcftools/0.1.14
source
/etc/profile.d/modules.sh
module load htslib/gcc/1.8 samtools/gcc/1.8 bcftools/gcc/1.8 bedtools/2.26.0 snpeff/4.3q vcftools/0.1.14
fi
export
PATH
=
/project/shared/bicf_workflow_ref/seqprg/bin:
$PATH
export
PATH
=
/project/shared/bicf_workflow_ref/seqprg/bin:
$PATH
mkdir
-p
temp
mkdir
-p
temp
...
@@ -146,7 +148,10 @@ then
...
@@ -146,7 +148,10 @@ then
java
-Xmx10g
-jar
$SNPEFF_HOME
/snpEff.jar
-no-intergenic
-lof
-c
$SNPEFF_HOME
/snpEff.config
${
snpeffgeno
}
lumpy.sv.vcf.gz | java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
" ( GEN[*].DV >= 20 )"
| bgzip
>
${
pair_id
}
.lumpy.vcf.gz
java
-Xmx10g
-jar
$SNPEFF_HOME
/snpEff.jar
-no-intergenic
-lof
-c
$SNPEFF_HOME
/snpEff.config
${
snpeffgeno
}
lumpy.sv.vcf.gz | java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
" ( GEN[*].DV >= 20 )"
| bgzip
>
${
pair_id
}
.lumpy.vcf.gz
elif
[[
$method
==
'pindel'
]]
elif
[[
$method
==
'pindel'
]]
then
then
module load pindel/0.2.5-intel
if
[[
-z
$isdocker
]]
then
module load pindel/0.2.5-intel
fi
genomefiledate
=
`
find
${
reffa
}
-maxdepth
0
-printf
"%TY%Tm%Td
\n
"
`
genomefiledate
=
`
find
${
reffa
}
-maxdepth
0
-printf
"%TY%Tm%Td
\n
"
`
touch
${
pair_id
}
.pindel.config
touch
${
pair_id
}
.pindel.config
for
i
in
*
.bam
;
do
for
i
in
*
.bam
;
do
...
...
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