itdseek memory, cnv b-allele freq code

variants/cnvkit.sh

@@ -30,7 +30,7 @@ baseDir="`dirname \"$0\"`"
 
 if [[ -z $index_path ]] 
 then
-    index_path='/project/shared/bicf_workflow_ref/human/GRCh38/clinseq_prj'
+    index_path='/project/shared/bicf_workflow_ref/human/GRCh38'
 fi
 # Check for mandatory options
 if [[ -z $pair_id ]] || [[ -z $sbam ]]
@@ -51,13 +51,18 @@ echo "${targets}antitargets.bed"
 echo "${normals}"
 
 source /etc/profile.d/modules.sh
-module load cnvkit/0.9.5 bedtools/2.26.0
+module load cnvkit/0.9.5 bedtools/2.26.0 samtools/gcc/1.8 bcftools/gcc/1.8
 unset DISPLAY
+
+#samtools index ${sbam}
+#bcftools mpileup --threads 10 -a 'INFO/AD,INFO/ADF,INFO/ADR,FORMAT/DP,FORMAT/SP,FORMAT/AD,FORMAT/ADF,FORMAT/ADR' -Ou -Q20 -d 99999 -C50 -f ${reffa} -t ${index_path}/NGSCheckMate.bed ${sbam} | bcftools call --threads 10 -vmO v -o common_variants.vcf
+
 cnvkit.py coverage ${sbam} ${targets}targets.bed -o ${pair_id}.targetcoverage.cnn
 cnvkit.py coverage ${sbam} ${targets}antitargets.bed -o ${pair_id}.antitargetcoverage.cnn
 cnvkit.py fix ${pair_id}.targetcoverage.cnn ${pair_id}.antitargetcoverage.cnn ${normals} -o ${pair_id}.cnr
 cnvkit.py segment ${pair_id}.cnr -o ${pair_id}.cns
 cnvkit.py call ${pair_id}.cns -o ${pair_id}.call.cns
+#cnvkit.py call ${pair_id}.cns -v common_variants.vcf -o ${pair_id}.ballelecall.cns
 cnvkit.py scatter ${pair_id}.cnr -s ${pair_id}.call.cns -t --segment-color "blue" -o ${pair_id}.cnv.scatter.pdf
 cut -f 1,2,3 ${pair_id}.call.cns | grep -v chrom | bedtools intersect -wao -b /project/shared/bicf_workflow_ref/human/GRCh38/cytoBand.txt -a stdin |cut -f 1,2,3,7 >  ${pair_id}.cytoband.bed
-perl $baseDir/filter_cnvkit.pl *.call.cns
+perl $baseDir/filter_cnvkit.pl ${pair_id}.call.cns

variants/itdseek.sh

@@ -52,4 +52,4 @@ stexe=`which samtools`
 
 samtools view -@ $SLURM_CPUS_ON_NODE -L ${itdbed} ${sbam} | /project/shared/bicf_workflow_ref/seqprg/itdseek-1.2/itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort | bedtools intersect -header -b ${itdbed} -a stdin | bgzip > ${pair_id}.itdseek.vcf.gz
 tabix ${pair_id}.itdseek.vcf.gz
-bcftools norm --fasta-ref $reffa -m - -Ov ${pair_id}.itdseek.vcf.gz | java -Xmx20g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 - |bgzip > ${pair_id}.itdseek_tandemdup.vcf.gz
+bcftools norm --fasta-ref $reffa -m - -Ov ${pair_id}.itdseek.vcf.gz | java -Xmx30g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 - |bgzip > ${pair_id}.itdseek_tandemdup.vcf.gz