test VEP

tasks/VEP.wdl

@@ -23,19 +23,15 @@ task VEP {
     set -e
     nt=$(nproc)
 
-    if [ only_pass ]; then
-      awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${sample_id}.INPUT.vcf
-    else
-      cp ${vcf} ${sample_id}.INPUT.vcf
-    fi
-
+    awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${sample_id}.PASS.vcf
+    
     # Extract the BND variants from VCF
-    # awk -F'\t' '{if(($1~"^#")||($8!~".*SVTYPE=BND.*")){print $0}}' ${sample_id}.INPUT.vcf > ${sample_id}.INPUT.vcf2maf.vcf
-    # awk -F'\t' '{if(($1~"^#")||($8~".*SVTYPE=BND.*")){print $0}}' ${sample_id}.INPUT.vcf > ${sample_id}.INPUT.VEP.vcf
+    # awk -F'\t' '{if(($1~"^#")||($8!~".*SVTYPE=BND.*")){print $0}}' ${sample_id}.PASS.vcf > ${sample_id}.PASS.vcf2maf.vcf
+    # awk -F'\t' '{if(($1~"^#")||($8~".*SVTYPE=BND.*")){print $0}}' ${sample_id}.PASS.vcf > ${sample_id}.INPUT.VEP.vcf
 
     # vcf2maf
     # perl ${vcf2maf_path}/vcf2maf.pl \
-    # --input-vcf ${sample_id}.INPUT.vcf2maf.vcf --output-maf ${basename}.maf \
+    # --input-vcf ${sample_id}.PASS.vcf2maf.vcf --output-maf ${basename}.maf \
     # --tumor-id ${tumor_id} --normal-id ${normal_id} \
     # --ref-fasta ${ref_dir}/${fasta} \
     # --vep-path ${vep_path} \
@@ -46,13 +42,14 @@ task VEP {
 
     # vep
     perl ${vep_path}/vep \
-    --input_file ${sample_id}.INPUT.vcf --output_file ${basename}.vep.vcf \
+    --input_file ${sample_id}.PASS.vcf --output_file ${basename}.vep.vcf \
     --fasta ${ref_dir}/${fasta} \
     --dir ${cache} \
     --assembly ${ncbi_build} \
     --species ${species} \
     --fork $nt \
-    --no_progress --no_stats --buffer_size 5000 --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --canonical --protein --biotype --uniprot --tsl --variant_class --shift_hgvs 1 --check_existing --total_length --allele_number --no_escape --xref_refseq --failed 1 --tab --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --format vcf --force_overwrite --offline --pubmed --regulatory
+    --format vcf --vcf \
+    --no_progress --no_stats --buffer_size 5000 --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --canonical --protein --biotype --uniprot --tsl --variant_class --shift_hgvs 1 --check_existing --total_length --allele_number --no_escape --xref_refseq --failed 1 --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --force_overwrite --offline --pubmed --regulatory
 
     # vcf2maf
     perl ${vcf2maf_path}/vcf2maf.pl \
@@ -60,10 +57,6 @@ task VEP {
     --input-vcf ${basename}.vep.vcf --output-maf ${basename}.maf \
     --tumor-id ${tumor_id} --normal-id ${normal_id} \
     --ref-fasta ${ref_dir}/${fasta} \
-    --vep-path ${vep_path} \
-    --vep-data ${cache} \
-    --ncbi-build ${ncbi_build} \
-    --species ${species} \
     --vep-fork $nt
   >>>
   
@@ -75,7 +68,7 @@ task VEP {
   }
 
   output {
-    File input_vcf = "${sample_id}.INPUT.vcf"
+    File input_vcf = "${sample_id}.PASS.vcf"
     File vep_vcf = "${basename}.vep.vcf"
     File maf = "${basename}.maf"
   }