SomaticSeq generated tumor-normal run scripts
Again, the detailed descriptions can be found here.
When you execute the commands described here, run scripts for the somatic mutation callers are generated.
Example command:
/home/fangl10/apps/somaticseq-2.7.2/utilities/dockered_pipelines/submit_callers_multiThreads.sh \
--normal-bam /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/BAMs/WGS_IL_N_1.bwa.dedup.bam \
--tumor-bam /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/tumorDesignate2N.bam \
--human-reference /sc1/groups/bfx-red/data/datainsights/SEQC2_Resources/GRCh38.d1.vd1.fa \
--dbsnp /sc1/groups/bfx-red/data/datainsights/SEQC2_Resources/dbSNP/dbsnp_146.hg38.vcf \
--threads 24 \
--truth-indel /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/synthetic_indels.leftAlign.vcf \
--truth-snv /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/synthetic_snvs.vcf \
--output-dir /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations \
--somaticseq-dir SomaticSeq.MSDUK.v2.7.2 \
--mutect2 --somaticsniper --vardict --muse --strelka --somaticseq
MuTect2 (script #12 out of 24, for each of the 24 threads)
#!/bin/bash
#$ -o /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/logs
#$ -e /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/logs
#$ -S /bin/bash
#$ -l h_vmem=8G
#$ -pe smp 4
set -e
echo -e "Start at `date +"%Y/%m/%d %H:%M:%S"`" 1>&2
tumor_name=`singularity exec --bind /:/mnt docker://lethalfang/samtools:0.1.18 samtools view -H /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/tumorDesignate2N.bam | egrep -w '^@RG' | grep -Po 'SM:[^\t$]+' | sed 's/SM://' | uniq | sed -e 's/[[:space:]]*$//'`
normal_name=`singularity exec --bind /:/mnt docker://lethalfang/samtools:0.1.18 samtools view -H /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/BAMs/WGS_IL_N_1.bwa.dedup.bam | egrep -w '^@RG' | grep -Po 'SM:[^\t$]+' | sed 's/SM://' | uniq | sed -e 's/[[:space:]]*$//'`
singularity exec --bind /:/mnt docker://broadinstitute/gatk:4.beta.6 \
java -Xmx7g -jar /gatk/gatk.jar Mutect2 \
--reference /mnt//sc1/groups/bfx-red/data/datainsights/SEQC2_Resources/GRCh38.d1.vd1.fa \
--intervals /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/12.bed \
--input /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/BAMs/WGS_IL_N_1.bwa.dedup.bam \
--input /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/tumorDesignate2N.bam \
--normalSampleName ${normal_name} \
--tumorSampleName ${tumor_name} \
--dbsnp /mnt//sc1/groups/bfx-red/data/datainsights/SEQC2_Resources/dbSNP/dbsnp_146.hg38.vcf \
--threads 4 \
\
--output /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/unfiltered.MuTect2.vcf
singularity exec --bind /:/mnt docker://broadinstitute/gatk:4.beta.6 \
java -Xmx7g -jar /gatk/gatk.jar FilterMutectCalls \
--variant /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/unfiltered.MuTect2.vcf \
\
--output /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/MuTect2.vcf
echo -e "Done at `date +"%Y/%m/%d %H:%M:%S"`" 1>&2
SomaticSniper
#!/bin/bash
#$ -o /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/logs
#$ -e /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/logs
#$ -S /bin/bash
#$ -l h_vmem=6G
set -e
echo -e "Start at `date +"%Y/%m/%d %H:%M:%S"`" 1>&2
singularity exec --bind /:/mnt docker://lethalfang/somaticsniper:1.0.5.0-2 \
/opt/somatic-sniper/build/bin/bam-somaticsniper \
-q 1 -Q 15 -s 0.00001 -F vcf \
-f /mnt//sc1/groups/bfx-red/data/datainsights/SEQC2_Resources/GRCh38.d1.vd1.fa \
/mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/tumorDesignate2N.bam \
/mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/BAMs/WGS_IL_N_1.bwa.dedup.bam \
/mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/SomaticSniper.vcf
i=1
while [[ $i -le 24 ]]
do
singularity exec --bind /:/mnt docker://lethalfang/bedtools:2.26.0 bash -c "bedtools intersect -a /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/SomaticSniper.vcf -b /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/${i}/${i}.bed -header | uniq > /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/${i}/SomaticSniper.vcf"
i=$(( $i + 1 ))
done
echo -e "Done at `date +"%Y/%m/%d %H:%M:%S"`" 1>&2
VarDict
#!/bin/bash
#$ -o /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/logs
#$ -e /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/logs
#$ -S /bin/bash
#$ -l h_vmem=14G
set -e
echo -e "Start at `date +"%Y/%m/%d %H:%M:%S"`" 1>&2
JAVA_HOME=''
singularity exec --bind /:/mnt docker://lethalfang/somaticseq:2.7.0 \
/opt/somaticseq/utilities/split_mergedBed.py \
-infile /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/12.bed -outfile /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/split_regions.bed
singularity exec --bind /:/mnt docker://lethalfang/vardictjava:1.5.1 bash -c \
"/opt/VarDict-1.5.1/bin/VarDict \
\
-G /mnt//sc1/groups/bfx-red/data/datainsights/SEQC2_Resources/GRCh38.d1.vd1.fa \
-f 0.05 -h \
-b '/mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/tumorDesignate2N.bam|/mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/BAMs/WGS_IL_N_1.bwa.dedup.bam' \
-Q 1 -c 1 -S 2 -E 3 -g 4 /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/split_regions.bed \
> /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/2017-12-06_13-13-27_896215295.var"
singularity exec --bind /:/mnt docker://lethalfang/vardictjava:1.5.1 \
bash -c "cat /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/2017-12-06_13-13-27_896215295.var | awk 'NR!=1' | /opt/VarDict/testsomatic.R | /opt/VarDict/var2vcf_paired.pl -N 'TUMOR|NORMAL' -f 0.05 \
> /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/VarDict.vcf"
echo -e "Done at `date +"%Y/%m/%d %H:%M:%S"`" 1>&2
MuSE
#!/bin/bash
#$ -o /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/logs
#$ -e /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/logs
#$ -S /bin/bash
#$ -l h_vmem=4G
set -e
echo -e "Start at `date +"%Y/%m/%d %H:%M:%S"`" 1>&2
cat /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/12.bed | awk -F "\t" '{print $1 "\t" $2 "\t" $3}' > /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/bed_3columns.bed
singularity exec --bind /:/mnt docker://marghoob/muse:1.0rc_c \
MuSEv1.0rc_submission_c039ffa call \
-O /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/MuSE \
-l /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/bed_3columns.bed \
-f /mnt//sc1/groups/bfx-red/data/datainsights/SEQC2_Resources/GRCh38.d1.vd1.fa \
/mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/tumorDesignate2N.bam \
/mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/BAMs/WGS_IL_N_1.bwa.dedup.bam
singularity exec --bind /:/mnt docker://marghoob/muse:1.0rc_c \
MuSEv1.0rc_submission_c039ffa sump \
-I /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/MuSE.MuSE.txt \
-G -O /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/MuSE.vcf \
-D /mnt//sc1/groups/bfx-red/data/datainsights/SEQC2_Resources/dbSNP/dbsnp_146.hg38.vcf.gz
echo -e "Done at `date +"%Y/%m/%d %H:%M:%S"`" 1>&2
Strelka
#!/bin/bash
#$ -o /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/logs
#$ -e /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/logs
#$ -S /bin/bash
#$ -l h_vmem=6G
set -e
echo -e "Start at `date +"%Y/%m/%d %H:%M:%S"`" 1>&2
singularity exec --bind /:/mnt docker://lethalfang/tabix:1.2.1 bash -c "cat /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/12.bed | bgzip > /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/12.bed.gz"
singularity exec --bind /:/mnt docker://lethalfang/tabix:1.2.1 tabix /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/12.bed.gz
singularity exec --bind /:/mnt docker://lethalfang/strelka:2.8.4 \
/opt/strelka/bin/configureStrelkaSomaticWorkflow.py \
--tumorBam=/mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/tumorDesignate2N.bam \
--normalBam=/mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/BAMs/WGS_IL_N_1.bwa.dedup.bam \
--referenceFasta=/mnt//sc1/groups/bfx-red/data/datainsights/SEQC2_Resources/GRCh38.d1.vd1.fa \
--callMemMb=6144 \
--region=chr8:24114336-145138636 --region=chr9:1-7654300 \
--callRegions=/mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/12.bed.gz \
\
--runDir=/mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/Strelka
singularity exec --bind /:/mnt docker://lethalfang/strelka:2.8.4 \
/mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/Strelka/runWorkflow.py -m local -j 1
echo -e "Done at `date +"%Y/%m/%d %H:%M:%S"`" 1>&2
SomaticSeq (automatically generated)
#!/bin/bash
#$ -o /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/SomaticSeq.MSDUK/logs
#$ -e /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/SomaticSeq.MSDUK/logs
#$ -S /bin/bash
#$ -l h_vmem=10G
set -e
echo -e "Start at `date +"%Y/%m/%d %H:%M:%S"`" 1>&2
singularity exec --bind /:/mnt docker://lethalfang/somaticseq:2.7.0 \
/opt/somaticseq/SomaticSeq.Wrapper.sh \
--output-dir /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/SomaticSeq.MSDUK \
--genome-reference /mnt//sc1/groups/bfx-red/data/datainsights/SEQC2_Resources/GRCh38.d1.vd1.fa \
--tumor-bam /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/tumorDesignate2N.bam \
--normal-bam /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/BAMs/WGS_IL_N_1.bwa.dedup.bam \
\
\
--mutect2 /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/MuTect2.vcf \
\
\
\
--sniper /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/SomaticSniper.vcf \
--vardict /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/VarDict.vcf \
--muse /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/MuSE.vcf \
\
\
\
--strelka-snv /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/Strelka/results/variants/somatic.snvs.vcf.gz \
--strelka-indel /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/Strelka/results/variants/somatic.indels.vcf.gz \
--inclusion-region /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/12.bed \
\
\
--dbsnp /mnt//sc1/groups/bfx-red/data/datainsights/SEQC2_Resources/dbSNP/dbsnp_146.hg38.vcf \
\
\
--truth-snv /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/synthetic_snvs.vcf \
--truth-indel /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/synthetic_indels.leftAlign.vcf \
\
\
--gatk /opt/GATK/GenomeAnalysisTK.jar
echo -e "Done at `date +"%Y/%m/%d %H:%M:%S"`" 1>&2
SomaticSeq with TNscope (created manually)
#!/bin/bash
#$ -o /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/SomaticSeq.MSDUKT.v2.7.2/logs
#$ -e /sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/SomaticSeq.MSDUKT.v2.7.2/logs
#$ -S /bin/bash
#$ -l h_vmem=10G
set -e
docker pull lethalfang/somaticseq:2.7.2
echo -e "Start at `date +"%Y/%m/%d %H:%M:%S"`" 1>&2
docker run --rm -v /:/mnt -u 83748 lethalfang/somaticseq:2.7.2 \
/opt/somaticseq/SomaticSeq.Wrapper.sh \
--output-dir /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/SomaticSeq.MSDUKT.v2.7.2 \
--genome-reference /mnt//sc1/groups/bfx-red/data/datainsights/SEQC2_Resources/GRCh38.d1.vd1.fa \
--tumor-bam /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/tumorDesignate2N.bam \
--normal-bam /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/BAMs/WGS_IL_N_1.bwa.dedup.bam \
--mutect2 /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/MuTect2.vcf \
--sniper /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/SomaticSniper.vcf \
--vardict /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/VarDict.vcf \
--muse /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/MuSE.vcf \
--tnscope /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/bwa.dedup-tumorDesignate.IL_N_2_vs_IL_N_1-TNScope.201711.02.vcf.gz \
--strelka-snv /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/Strelka/results/variants/somatic.snvs.vcf.gz \
--strelka-indel /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/Strelka/results/variants/somatic.indels.vcf.gz \
--inclusion-region /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/somaticMutations/12/12.bed \
--dbsnp /mnt//sc1/groups/bfx-red/data/datainsights/SEQC2_Resources/dbSNP/dbsnp_146.hg38.vcf \
--truth-snv /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/synthetic_snvs.vcf \
--truth-indel /mnt//sc1/groups/bfx-red/analysis/datainsights/projects/SEQC2/wg1/bamSims/bwa.IL1N_vs_IL2N/synthetic_indels.leftAlign.vcf \
echo -e "Done at `date +"%Y/%m/%d %H:%M:%S"`" 1>&2