更新 'tasks/filter_vep_annovar.wdl'

exclude ,

tasks/filter_vep_annovar.wdl

@@ -16,16 +16,18 @@ task filter_vep_annovar{
         mkdir ./prepare/
  
         vep_index=`echo ${vep_vcf}|awk -F "/" '{print $NF}'`
+        vep_id=`echo ${vep_vcf}|awk -F "/" '{print $NF}'|sed 's/\.vcf//'`
+        
         echo ${sample_id}
-        perl /software/convert2annovar.pl -format vcf4 ${vep_vcf}  -outfile prepare/$vep_index.avinput -allsample -withfreq -include
+        awk -F "\t" '{if(!($5~/,/))print}' ${vep_vcf} > ./prepare/$vep_id.only.vcf
+        perl /software/convert2annovar.pl -format vcf4 ./prepare/$vep_id.only.vcf  -outfile prepare/$vep_index.avinput -allsample -withfreq -include
         echo "uid" > ./prepare/$vep_index.avinput_uid.txt
         cut -f 1-5 prepare/$vep_index.avinput | sed 's/\t/_/g' >> prepare/$vep_index.avinput_uid.txt
-        sed '1,1000s/^#CHROM/CHROM/' ${vep_vcf} |grep -v "#" > prepare/$vep_index.clean.txt
+        sed '1,1000s/^#CHROM/CHROM/' ./prepare/$vep_id.only.vcf |grep -v "#" > prepare/$vep_index.clean.txt
         paste prepare/$vep_index.avinput_uid.txt prepare/$vep_index.clean.txt > prepare/$vep_index.add_uid.txt
         Rscript /software/filter.R  --vep_file prepare/$vep_index.add_uid.txt --annovar_file ${annovar_txt}
         python /software/filter.py --uid_list prepare/annovar_uid.txt --vep_vcf prepare/$vep_index.add_uid.txt
-        vep_id=`echo $vep_index|sed 's/.vcf//'`
-        sed '1,1000s/^#CHROM/CHROM/' ${vep_vcf} |grep  "#"  > output/$vep_id.filter.vcf
+        sed '1,1000s/^#CHROM/CHROM/' ./prepare/$vep_id.only.vcf |grep  "#"  > output/$vep_id.filter.vcf
         sed '1s/^CHROM/#CHROM/' prepare/$vep_id.filter_prepare.vcf >> output/$vep_id.filter.vcf
         rm output/$vep_id.removed.vcf