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process_scripts
Commits
f7278ea1
Commit
f7278ea1
authored
6 years ago
by
Brandi Cantarel
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add pindel
parent
8140bbee
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variants/svcalling.sh
+67
-82
67 additions, 82 deletions
variants/svcalling.sh
with
67 additions
and
82 deletions
variants/svcalling.sh
+
67
−
82
View file @
f7278ea1
...
...
@@ -11,14 +11,16 @@ usage() {
exit
1
}
OPTIND
=
1
# Reset OPTIND
while
getopts
:r:
a
:b:
n:k:p
:h opt
while
getopts
:r:
p
:b:
t:i:k:n:m
:h opt
do
case
$opt
in
r
)
index_path
=
$OPTARG
;;
p
)
pair_id
=
$OPTARG
;;
b
)
sbam
=
$OPTARG
;;
k
)
keepid
=
$OPTARG
;;
k
)
tid
=
$OPTARG
;;
i
)
nid
=
$OPTARG
;;
n
)
normal
=
$OPTARG
;;
m
)
method
=
$OPTARG
;;
h
)
usage
;;
esac
done
...
...
@@ -50,92 +52,75 @@ source /etc/profile.d/modules.sh
module load speedseq/20160506 novoBreak/v1.1.3 delly2/v0.7.7-multi samtools/1.6 bedtools/2.26.0 snpeff/4.3q vcftools/0.1.14
mkdir
temp
#if [[ -n ${normal} ]]
#then
#run_novoBreak.sh /cm/shared/apps/novoBreak/novoBreak_distribution_v1.1.3rc ${reffa} ${sbam} ${normal} $SLURM_CPUS_ON_NODE
#perl $baseDir/vcf2bed.sv.pl novoBreak.pass.flt.vcf |sort -T temp -V -k 1,1 -k 2,2n > novobreak.bed
#mv novoBreak.pass.flt.vcf ${pair_id}.novobreak.vcf
#bgzip ${pair_id}.novobreak.vcf
#fi
if
[[
-n
${
normal
}
]]
genomefiledate
=
`
find
${
reffa
}
-maxdepth
0
-printf
"%TY%Tm%Td
\n
"
`
if
[[
$method
==
'pindel'
]]
then
#RUN DELLY
delly2 call
-t
BND
-o
delly_translocations.bcf
-q
30
-g
${
reffa
}
${
sbam
}
${
normal
}
delly2 call
-t
DUP
-o
delly_duplications.bcf
-q
30
-g
${
reffa
}
${
sbam
}
${
normal
}
delly2 call
-t
INV
-o
delly_inversions.bcf
-q
30
-g
${
reffa
}
${
sbam
}
${
normal
}
delly2 call
-t
DEL
-o
delly_deletion.bcf
-q
30
-g
${
reffa
}
${
sbam
}
${
normal
}
delly2 call
-t
INS
-o
delly_insertion.bcf
-q
30
-g
${
reffa
}
${
sbam
}
${
normal
}
delly2 filter
-t
BND
-o
delly_tra.bcf
-f
somatic
-s
samples.tsv delly_translocations.bcf
delly2 filter
-t
DUP
-o
delly_dup.bcf
-f
somatic
-s
samples.tsv delly_duplications.bcf
delly2 filter
-t
INV
-o
delly_inv.bcf
-f
somatic
-s
samples.tsv delly_inversions.bcf
delly2 filter
-t
DEL
-o
delly_del.bcf
-f
somatic
-s
samples.tsv delly_deletion.bcf
delly2 filter
-t
INS
-o
delly_ins.bcf
-f
somatic
-s
samples.tsv delly_insertion.bcf
else
#RUN DELLY
delly2 call
-t
BND
-o
delly_translocations.bcf
-q
30
-g
${
reffa
}
${
sbam
}
delly2 call
-t
DUP
-o
delly_duplications.bcf
-q
30
-g
${
reffa
}
${
sbam
}
delly2 call
-t
INV
-o
delly_inversions.bcf
-q
30
-g
${
reffa
}
${
sbam
}
delly2 call
-t
DEL
-o
delly_deletion.bcf
-q
30
-g
${
reffa
}
${
sbam
}
delly2 call
-t
INS
-o
delly_insertion.bcf
-q
30
-g
${
reffa
}
${
sbam
}
delly2 filter
-t
BND
-o
delly_tra.bcf
-f
germline delly_translocations.bcf
delly2 filter
-t
DUP
-o
delly_dup.bcf
-f
germline delly_duplications.bcf
delly2 filter
-t
INV
-o
delly_inv.bcf
-f
germline delly_inversions.bcf
delly2 filter
-t
DEL
-o
delly_del.bcf
-f
germline delly_deletion.bcf
delly2 filter
-t
INS
-o
delly_ins.bcf
-f
germline delly_insertion.bcf
module load samtools/1.6 pindel/0.2.5-intel snpeff/4.3q
echo
-e
"
${
sbam
}
\t
400
\t
${
tid
}
"
>
${
pair_id
}
.pindel.config
if
[[
-n
${
normal
}
]]
then
echo
-e
"
${
normal
}
\t
400
\t
${
nid
}
"
>>
${
pair_id
}
.pindel.config
fi
pindel
-T
$SLURM_CPUS_ON_NODE
-f
${
reffa
}
-i
${
pair_id
}
.pindel.config
-o
${
pair_id
}
.pindel_out
--RP
pindel2vcf
-P
${
pair_id
}
.pindel_out
-r
${
reffa
}
-R
HG38
-d
${
genomefiledate
}
-v
pindel.vcf
java
-Xmx10g
-jar
$SNPEFF_HOME
/snpEff.jar
-no-intergenic
-lof
-c
$SNPEFF_HOME
/snpEff.config GRCh38.86 pindel.vcf | java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
" ( GEN[*].AD[1] >= 20 )"
| bgzip
>
${
pair_id
}
.pindel.vcf.gz
fi
#MERGE DELLY AND MAKE BED
bcftools concat
-a
-O
v delly_dup.bcf delly_inv.bcf delly_tra.bcf delly_del.bcf delly_ins.bcf| vcf-sort
-t
temp
>
delly.vcf
perl
$baseDir
/vcf2bed.sv.pl delly.vcf |
sort
-V
-k
1,1
-k
2,2n
>
delly.bed
bgzip delly.vcf
if
[[
-n
${
normal
}
]]
if
[[
$method
==
'delly'
]]
then
tabix delly.vcf.gz
bcftools view
-O
z
-o
${
pair_id
}
.delly.vcf.gz
-s
${
keepid
}
delly.vcf.gz
else
mv
delly.vcf.gz
${
pair_id
}
.delly.vcf.gz
module load delly2/v0.7.7-multi samtools/1.6 snpeff/4.3q
if
[[
-n
${
normal
}
]]
then
#RUN DELLY
echo
-e
"
${
normal
}
\t
control"
>
samples.tsv
echo
-e
"
${
tumor
}
\t
tumor"
>>
samples.tsv
delly2 call
-t
BND
-o
delly_translocations.bcf
-q
30
-g
${
reffa
}
${
sbam
}
${
normal
}
delly2 call
-t
DUP
-o
delly_duplications.bcf
-q
30
-g
${
reffa
}
${
sbam
}
${
normal
}
delly2 call
-t
INV
-o
delly_inversions.bcf
-q
30
-g
${
reffa
}
${
sbam
}
${
normal
}
delly2 call
-t
DEL
-o
delly_deletion.bcf
-q
30
-g
${
reffa
}
${
sbam
}
${
normal
}
delly2 call
-t
INS
-o
delly_insertion.bcf
-q
30
-g
${
reffa
}
${
sbam
}
${
normal
}
delly2 filter
-t
BND
-o
delly_tra.bcf
-f
somatic
-s
samples.tsv delly_translocations.bcf
delly2 filter
-t
DUP
-o
delly_dup.bcf
-f
somatic
-s
samples.tsv delly_duplications.bcf
delly2 filter
-t
INV
-o
delly_inv.bcf
-f
somatic
-s
samples.tsv delly_inversions.bcf
delly2 filter
-t
DEL
-o
delly_del.bcf
-f
somatic
-s
samples.tsv delly_deletion.bcf
delly2 filter
-t
INS
-o
delly_ins.bcf
-f
somatic
-s
samples.tsv delly_insertion.bcf
else
#RUN DELLY
delly2 call
-t
BND
-o
delly_translocations.bcf
-q
30
-g
${
reffa
}
${
sbam
}
delly2 call
-t
DUP
-o
delly_duplications.bcf
-q
30
-g
${
reffa
}
${
sbam
}
delly2 call
-t
INV
-o
delly_inversions.bcf
-q
30
-g
${
reffa
}
${
sbam
}
delly2 call
-t
DEL
-o
delly_deletion.bcf
-q
30
-g
${
reffa
}
${
sbam
}
delly2 call
-t
INS
-o
delly_insertion.bcf
-q
30
-g
${
reffa
}
${
sbam
}
delly2 filter
-t
BND
-o
delly_tra.bcf
-f
germline delly_translocations.bcf
delly2 filter
-t
DUP
-o
delly_dup.bcf
-f
germline delly_duplications.bcf
delly2 filter
-t
INV
-o
delly_inv.bcf
-f
germline delly_inversions.bcf
delly2 filter
-t
DEL
-o
delly_del.bcf
-f
germline delly_deletion.bcf
delly2 filter
-t
INS
-o
delly_ins.bcf
-f
germline delly_insertion.bcf
fi
#MERGE DELLY AND MAKE BED
bcftools concat
-a
-O
v delly_dup.bcf delly_inv.bcf delly_tra.bcf delly_del.bcf delly_ins.bcf| vcf-sort
-t
temp
>
delly.vcf
bgzip delly.vcf
java
-Xmx10g
-jar
$SNPEFF_HOME
/snpEff.jar
-no-intergenic
-lof
-c
$SNPEFF_HOME
/snpEff.config GRCh38.86 delly.vcf | java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
" ( GEN[*].AD[1] >= 20 )"
| bgzip
>
${
pair_id
}
.delly.vcf.gz
fi
tabix
${
pair_id
}
.delly.vcf.gz
#MAKE FILES FOR LUMPY
samtools
sort
-@
$SLURM_CPUS_ON_NODE
-n
-o
namesort.bam
${
sbam
}
samtools view
-h
namesort.bam | samblaster
-M
-a
--excludeDups
--addMateTags
--maxSplitCount
2
--minNonOverlap
20
-d
discordants.sam
-s
splitters.sam
>
temp.sam
gawk
'{ if ($0~"^@") { print; next } else { $10="*"; $11="*"; print } }'
OFS
=
"
\t
"
splitters.sam | samtools view
-S
-b
- | samtools
sort
-o
splitters.bam -
gawk
'{ if ($0~"^@") { print; next } else { $10="*"; $11="*"; print } }'
OFS
=
"
\t
"
discordants.sam | samtools view
-S
-b
- | samtools
sort
-o
discordants.bam -
#RUN LUMPY
if
[[
-n
${
normal
}
]]
if
[[
$method
==
'lumpy'
]]
then
samtools
sort
-@
$SLURM_CPUS_ON_NODE
-n
-o
namesort.bam
${
normal
}
#MAKE FILES FOR LUMPY
samtools
sort
-@
$SLURM_CPUS_ON_NODE
-n
-o
namesort.bam
${
sbam
}
samtools view
-h
namesort.bam | samblaster
-M
-a
--excludeDups
--addMateTags
--maxSplitCount
2
--minNonOverlap
20
-d
discordants.sam
-s
splitters.sam
>
temp.sam
gawk
'{ if ($0~"^@") { print; next } else { $10="*"; $11="*"; print } }'
OFS
=
"
\t
"
splitters.sam | samtools view
-S
-b
- | samtools
sort
-o
normal.splitters.bam -
gawk
'{ if ($0~"^@") { print; next } else { $10="*"; $11="*"; print } }'
OFS
=
"
\t
"
discordants.sam | samtools view
-S
-b
- | samtools
sort
-o
normal.discordants.bam -
speedseq sv
-t
$SLURM_CPUS_ON_NODE
-o
sssv
-R
${
reffa
}
-B
${
normal
}
,
${
sbam
}
-D
normal.discordants.bam,discordants.bam
-S
normal.splitters.bam,splitters.bam
-x
${
index_path
}
/exclude_alt.bed
java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
-n
"GEN[0].SU > 1"
sssv.sv.vcf.gz |bgzip
>
tumor.sssv.sv.vcf.gz
tabix tumor.sssv.sv.vcf.gz
bcftools view
-O
z
-o
${
pair_id
}
.sssv.sv.vcf.gz
-s
${
keepid
}
tumor.sssv.sv.vcf.gz
else
speedseq sv
-t
$SLURM_CPUS_ON_NODE
-o
${
pair_id
}
.sssv
-R
${
reffa
}
-B
${
sbam
}
-D
discordants.bam
-S
splitters.bam
-x
${
index_path
}
/exclude_alt.bed
gawk
'{ if ($0~"^@") { print; next } else { $10="*"; $11="*"; print } }'
OFS
=
"
\t
"
splitters.sam | samtools view
-S
-b
- | samtools
sort
-o
splitters.bam -
gawk
'{ if ($0~"^@") { print; next } else { $10="*"; $11="*"; print } }'
OFS
=
"
\t
"
discordants.sam | samtools view
-S
-b
- | samtools
sort
-o
discordants.bam -
#RUN LUMPY
if
[[
-n
${
normal
}
]]
then
samtools
sort
-@
$SLURM_CPUS_ON_NODE
-n
-o
namesort.bam
${
normal
}
samtools view
-h
namesort.bam | samblaster
-M
-a
--excludeDups
--addMateTags
--maxSplitCount
2
--minNonOverlap
20
-d
discordants.sam
-s
splitters.sam
>
temp.sam
gawk
'{ if ($0~"^@") { print; next } else { $10="*"; $11="*"; print } }'
OFS
=
"
\t
"
splitters.sam | samtools view
-S
-b
- | samtools
sort
-o
normal.splitters.bam -
gawk
'{ if ($0~"^@") { print; next } else { $10="*"; $11="*"; print } }'
OFS
=
"
\t
"
discordants.sam | samtools view
-S
-b
- | samtools
sort
-o
normal.discordants.bam -
speedseq sv
-t
$SLURM_CPUS_ON_NODE
-o
lumpy
-R
${
reffa
}
-B
${
normal
}
,
${
sbam
}
-D
normal.discordants.bam,discordants.bam
-S
normal.splitters.bam,splitters.bam
-x
${
index_path
}
/exclude_alt.bed
else
speedseq sv
-t
$SLURM_CPUS_ON_NODE
-o
lumpy
-R
${
reffa
}
-B
${
sbam
}
-D
discordants.bam
-S
splitters.bam
-x
${
index_path
}
/exclude_alt.bed
fi
java
-Xmx10g
-jar
$SNPEFF_HOME
/snpEff.jar
-no-intergenic
-lof
-c
$SNPEFF_HOME
/snpEff.config GRCh38.86 lumpy.sv.vcf.gz | java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
" ( GEN[*].DV >= 20 )"
| bgzip
>
${
pair_id
}
.lumpy.vcf.gz
fi
java
-jar
$SNPEFF_HOME
/SnpSift.jar filter
"GEN[0].SU > 10"
${
pair_id
}
.sssv.sv.vcf.gz
>
lumpy.vcf
perl
$baseDir
/vcf2bed.sv.pl lumpy.vcf
>
lumpy.bed
#COMPARE DELLY & LUMPY
#if [[ -n ${normal} ]]
#then
#bedtools multiinter -cluster -header -names novobreak delly lumpy -i novobreak.bed delly.bed lumpy.bed > sv.intersect.bed
#zcat ${pair_id}.novobreak.vcf.gz | perl -p -e 's/SPIKEIN/${tid}/' |bgzip > svt1.vcf.gz
#grep novobreak sv.intersect.bed |cut -f 1,2,3 |sort -V -k 1,1 -k 2,2n |grep -v start | bedtools intersect -header -b stdin -a ${pair_id}.novobreak.vcf.gz | perl -p -e 's/SPIKEIN/${tid}/' |bgzip > svt1.vcf.gz
#else
#fi
bedtools multiinter
-cluster
-header
-names
delly lumpy
-i
delly.bed lumpy.bed
>
sv.intersect.bed
grep
delly sv.intersect.bed |cut
-f
1,2,3 |sort
-V
-k
1,1
-k
2,2n |grep
-v
'start'
|grep
-v
'novobreak'
| bedtools intersect
-header
-b
stdin
-a
${
pair_id
}
.delly.vcf.gz |bgzip
>
svt2.vcf.gz
grep
lumpy sv.intersect.bed |cut
-f
1,2,3 |sort
-V
-k
1,1
-k
2,2n |grep
-v
'start'
|grep
-v
'delly'
|grep
-v
'novobreak'
| bedtools intersect
-header
-b
stdin
-a
${
pair_id
}
.sssv.sv.vcf.gz |bgzip
>
svt3.vcf.gz
vcf-concat svt
*
.vcf.gz | vcf-sort
-t
temp
>
${
pair_id
}
.sv.vcf
java
-Xmx10g
-jar
$SNPEFF_HOME
/snpEff.jar
-no-intergenic
-lof
-c
$SNPEFF_HOME
/snpEff.config GRCh38.86
${
pair_id
}
.sv.vcf
>
${
pair_id
}
.sv.annot.vcf
perl
$baseDir
/svannot.pl
-i
${
pair_id
}
.sv.annot.vcf
bgzip
${
pair_id
}
.sv.annot.vcf
tabix
${
pair_id
}
.sv.annot.vcf.gz
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