java -jar cromwell.jar run variantEffectPredictor.wdl --inputs inputs.json

     CHR_LEN=$(zcat ~{inputVcf} | head -n 800 | grep contig | grep -w ~{chromosome} | grep -v _ | sed -r 's/.*length=([[:digit:]]+)./\1/')
     LARGEST=$(zcat ~{inputVcf} | head -n 800 | grep contig | grep -v _ | sed -r 's/.*length=([[:digit:]]+)./\1/' | sort -n | tail -n 1)
     echo | awk -v chr_len=$CHR_LEN -v largest_chr=$LARGEST '{print int((chr_len/largest_chr + 0.1) * 10)/10}'

     set -euo pipefail
 
     bedtools intersect -header -u \
                        -a ~{vcfFile} \
                        -b ~{targetBed} \
                        > ~{basename}.targeted.vcf
 
     bgzip -c ~{basename}.targeted.vcf > ~{basename}.targeted.vcf.gz
 
     tabix -p vcf ~{basename}.targeted.vcf.gz

     zgrep -v ^# ~{vcfFile} | cut -f 1 | uniq

     set -euo pipefail
     bcftools view -r ~{regions} ~{vcfFile} | bgzip -c > ~{basename}.vcf.gz

     set -euo pipefail
 
     if [ "~{species}" = "homo_sapiens" ]; then
       human_only_command_line="--polyphen b --af --af_1kg --af_esp --af_gnomad"
     else
       human_only_command_line=""
     fi
 
     if ~{vepStats} ; then
       vepStats_command_line=""
     else 
       vepStats_command_line="--no_stats"
     fi
 
 
     vep --offline --dir ~{vepCacheDir} -i ~{vcfFile} --fasta ~{referenceFasta} --species ~{species} \
           --assembly ~{ncbiBuild} -o ~{basename}.vep.vcf.gz --vcf --compress_output bgzip ~{addParam} \
           --no_progress --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --mane \
           --canonical --protein --biotype --uniprot --tsl --variant_class --check_existing --total_length \
           --allele_number --no_escape --xref_refseq --failed 1 --flag_pick_allele \
           --pick_order canonical,tsl,biotype,rank,ccds,length \
           $vepStats_command_line \
           $human_only_command_line \
           --pubmed --fork 4 --regulatory
 

     set -euo pipefail
 
     TUMR="~{tumorName}"
 
     if [ -z "~{normalName}" ]; then
         NORM="unmatched";
     else NORM="~{normalName}";
     fi
 
     echo $TUMR > names.txt
     echo $NORM >> names.txt
 

     set -euo pipefail
 
     if ~{updateTagValue} ; then
         zcat ~{vcfFile} | sed s/Number\=A/Number\=./ | sed s/Number\=R/Number\=./ > "~{basename}_temporary.vcf"
         cat ~{basename}_temporary.vcf | sed 's/QSS\,Number\=A/QSS\,Number\=\./' | sed 's/AS_FilterStatus\,Number\=A/AS_FilterStatus\,Number\=\./' | bgzip -c > "~{basename}_input.vcf.gz"
     else
         zcat ~{vcfFile} | sed 's/QSS\,Number\=A/QSS\,Number\=\./' | sed 's/AS_FilterStatus\,Number\=A/AS_FilterStatus\,Number\=\./' | bgzip -c > "~{basename}_input.vcf.gz"
     fi
 
     tabix -p vcf "~{basename}_input.vcf.gz"
 
     cat ~{tumorNormalNames} > "~{basename}_header"
     bcftools merge "~{basename}_input.vcf.gz" "~{basename}_input.vcf.gz" --force-samples > "~{basename}.temp_tumor.vcf"
     bcftools reheader -s "~{basename}_header" "~{basename}.temp_tumor.vcf" > "~{basename}.unmatched.vcf"
     bgzip -c "~{basename}.unmatched.vcf" > "~{basename}.unmatched.vcf.gz"
     tabix -p vcf "~{basename}.unmatched.vcf.gz"

     set -euo pipefail
 
     TUMR=$(sed -n 1p ~{tumorNormalNames} )
     NORM=$(sed -n 2p ~{tumorNormalNames} )
 
     bgzip -c -d ~{vcfFile} > ~{basename}
 
     if ~{retainInfoProvided} ; then
         retainInfo_command_line="--retain-info MBQ,MMQ,TLOD,set"
     else
         retainInfo_command_line=""
     fi
 
     vcf2maf --ref-fasta ~{referenceFasta} --species ~{species} --ncbi-build ~{ncbiBuild} \
             --input-vcf ~{basename} --output-maf ~{basename}.maf \
             --tumor-id $TUMR --normal-id $NORM --vcf-tumor-id $TUMR --vcf-normal-id $NORM \
             --vep-path ~{vepPath} --vep-data ~{vepCacheDir} \
             --min-hom-vaf ~{minHomVaf} --buffer-size ~{bufferSize} \
             $retainInfo_command_line \
             --vep-stats ~{vepStats}

     set -euo pipefail
 
     head -n 2 ~{mafs[0]} > ~{basename}
     cat ~{sep=" " mafs} | grep -v ^# | grep -v "Hugo_Symbol" >> ~{basename}
     bgzip -c ~{basename} > ~{basename}.maf.gz

     set -euo pipefail
 
     gatk --java-options "-Xmx~{jobMemory - overhead}G" MergeVcfs \
     -I ~{sep=" -I " vcfs} ~{extraArgs} \
     -O ~{basename}.vcf.gz