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