lancet update

variants/somatic_vc.sh

@@ -80,7 +80,7 @@ baseDir="`dirname \"$0\"`"
 
 if [ $algo == 'strelka2' ]
   then
-    module load strelka/2.8.3 manta/1.2.0 snpeff/4.3q vcftools/0.1.14
+    module load strelka/2.8.3 samtools/1.6 manta/1.2.0 snpeff/4.3q vcftools/0.1.14
     mkdir manta strelka
     configManta.py --normalBam ${normal} --tumorBam ${tumor} --referenceFasta ${reffa} --runDir manta
     manta/runWorkflow.py -m local -j 8
@@ -91,7 +91,7 @@ fi
 
 if [ $algo == 'virmid' ]
   then 
-    module load snpeff/4.3q virmid/1.2 vcftools/0.1.14
+    module load snpeff/4.3q virmid/1.2 samtools/1.6 vcftools/0.1.14
     virmid -R ${reffa} -D ${tumor} -N ${normal} -s ${cosmic} -t $SLURM_CPUS_ON_NODE -M 2000 -c1 10 -c2 10
     perl $baseDir/addgt_virmid.pl ${tumor}.virmid.som.passed.vcf
     perl $baseDir/addgt_virmid.pl ${tumor}.virmid.loh.passed.vcf
@@ -100,14 +100,14 @@ fi
 
 if [ $algo == 'speedseq' ]
   then 
-    module load snpeff/4.3q speedseq/20160506 vcftools/0.1.14
+    module load snpeff/4.3q speedseq/20160506 samtools/1.6 vcftools/0.1.14
     speedseq somatic -q 10 -t $SLURM_CPUS_ON_NODE -o sssom ${reffa} ${normal} ${tumor}
     vcf-annotate -H -n --fill-type sssom.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar filter '((QUAL >= 10) & (GEN[*].DP >= 10))' | perl -pe 's/TUMOR/${tid}/' | perl -pe 's/NORMAL/${nid}/g' |bgzip > ${pair_id}.sssom.vcf.gz
 fi
 
 if [ $algo == 'mutect2' ]
 then
-  module load parallel gatk/3.7 snpeff/4.3q vcftools/0.1.14
+  module load parallel gatk/3.7 snpeff/4.3q samtools/1.6 vcftools/0.1.14
   cut -f 1 ${index_path}/genomefile.5M.txt | parallel --delay 2 -j 10 "java -Xmx20g -jar \$GATK_JAR -R ${reffa} -D ${dbsnp} -T MuTect2 -stand_call_conf 10 -A FisherStrand -A QualByDepth -A VariantType -A DepthPerAlleleBySample -A HaplotypeScore -A AlleleBalance -I:tumor ${tumor} -I:normal ${normal} --cosmic ${cosmic} -o ${tid}.{}.mutect.vcf -L {}"
   vcf-concat ${tid}*.vcf | vcf-sort | vcf-annotate -n --fill-type | java -jar \$SNPEFF_HOME/SnpSift.jar filter -p '((FS <= 60) & GEN[*].DP >= 10)' | perl -pe 's/TUMOR/${tid}/' | perl -pe 's/NORMAL/${nid}/g' |bgzip > ${pair_id}.pmutect.vcf.gz
 fi
@@ -115,8 +115,8 @@ fi
 if [ $algo == 'varscan' ]
 then
   module load snpeff/4.3q samtools/1.6 VarScan/2.4.2 speedseq/20160506 vcftools/0.1.14
-  sambamba mpileup -t $SLURM_CPUS_ON_NODE ${tumor} --samtools "-C 50 -f ${reffa}"  > t.mpileup
-  sambamba mpileup -t $SLURM_CPUS_ON_NODE ${normal} --samtools "-C 50 -f ${reffa}"  > n.mpileup
+  sambamba mpileup --tmpdir=./ -t $SLURM_CPUS_ON_NODE ${tumor} --samtools "-C 50 -f ${reffa}"  > t.mpileup
+  sambamba mpileup --tmpdir=./ -t $SLURM_CPUS_ON_NODE ${normal} --samtools "-C 50 -f ${reffa}"  > n.mpileup
   VarScan somatic n.mpileup t.mpileup vscan --output-vcf 1
   VarScan copynumber n.mpileup t.mpileup vscancnv 
   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 > ${tid}_${nid}.varscan.vcf.gz
@@ -124,7 +124,7 @@ fi
 
 if [ $algo == 'shimmer' ]
 then
-    module load snpeff/4.3q shimmer/0.1.1 vcftools/0.1.14
+    module load snpeff/4.3q shimmer/0.1.1 samtools/1.6  vcftools/0.1.14
     shimmer.pl --minqual 25 --ref ${reffa} ${normal} ${tumor} --outdir shimmer 2> shimmer.err
     perl /project/PHG/PHG_Clinical/clinseq_workflows/scripts/add_readct_shimmer.pl
     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
@@ -132,7 +132,7 @@ fi
 
 if [ $algo == 'lancet' ]
 then
-    module load snpeff/4.3q lancet vcftools/0.1.14
-    lancet --tumor ${tumor} --normal ${normal} --ref $reffa -B $tbed --num-threads 16 > lancet.vcf
-    vcf-sort lancet.vcf | vcf-annotate -n --fill-type -n | perl -pe 's/TUMOR/${tid}/' | perl -pe 's/NORMAL/${nid}/g' |bgzip > ${pair_id}.lancet.vcf.gz
+    module load snpeff/4.3q lancet samtools/1.6 vcftools/0.1.14
+    lancet --tumor ${tumor} --normal ${normal} --ref $reffa -B $tbed --num-threads $SLURM_CPUS_ON_NODE > lancet.vcf
+    vcf-sort lancet.vcf | vcf-annotate -n --fill-type -n | java -jar $SNPEFF_HOME/SnpSift.jar filter "((FILTER = 'PASS') | (FILTER = 'LowVafTumor') | (FILTER = 'LowVafTumor;LowAltCntTumor')) & (GEN[*].DP >= 10)" |bgzip > ${pair_id}.lancet.vcf.gz
 fi