remove ad

tasks/benchmark.wdl

 		export HGREF=/cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa
 
 		cat ${vcf} | grep '#' > header
-		cat ${vcf} | grep -v '#' | grep -v '0/0' | grep -v '\./\.' > body
+		cat ${vcf} | grep -v '#' | grep -v '0/0' | grep -v '\./\.'| awk '
+		    BEGIN { OFS = "\t" }
+		     { 
+		        for ( i=9; i<=NF; i++ ) { 
+		            split($i,a,":") ;$i = a[1];
+		        } 
+		    } 
+		    { print }
+		' > body
 		cat header body > filtered.vcf
 
 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip filtered.vcf -c > ${sample}.rtg.vcf.gz