replicate ji

tasks/jaccard_index.wdl

@@ -10,8 +10,13 @@ task JI {
 	command <<<
 		set -o pipefail
 		set -e
+		rtg bgzip ${vcf_a} -c > vcf_a.vcf.gz
+		rtg index vcf_a.vcf.gz
 
-		rtg vcfeval -b ${vcf_a} -c ${vcf_b} -o ${dir_name} -t ${sdf}
+		rtg bgzip ${vcf_b} -c > vcf_b.vcf.gz
+		rtg index vcf_b.vcf.gz
+
+		rtg vcfeval -b vcf_a.vcf.gz -c vcf_b.vcf.gz -o ${dir_name} -t ${sdf}
 		mv ${dir_name}/summary.txt ${dir_name}.txt
 
 	>>>