immune

tasks/annovar.wdl

@@ -2,6 +2,7 @@ task annovar {
 
 	File vcf_file
 	File database
+	File immune_txt
 	String sample
 	String docker
 	String cluster_config
@@ -11,6 +12,10 @@ task annovar {
 	command <<<
 		nt=$(nproc)
 		/installations/annovar/table_annovar.pl ${vcf_file} ${database} -buildver hg38 -out ${sample} -remove -protocol refGene,ensGene,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad30_genome,1000g2015aug_all,clinvar_20190305,gnomad211_genome -operation g,g,f,f,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
+
+		awk 'NR==FNR{a[$1]=$2;next} ($7) in a{print $0}' ${immune_txt} ${sample}.hg38_multianno.txt > ${sample}.filtered
+
+		cat ${sample}.hg38_multianno.txt | head -n1 | cat -  ${sample}.filtered > ${sample}_immune.hg38_multianno.txt
 	>>>
 
 	runtime {
@@ -23,6 +28,7 @@ task annovar {
 		File avinput = "${sample}.avinput"
 		File multianno_txt = "${sample}.hg38_multianno.txt"
 		File multianno_vcf = "${sample}.hg38_multianno.vcf"
+		File immune_annovar_txt = "${sample}_immune.hg38_multianno.txt"
 
 	}
 }