diff --git a/core/src/main/scala/org/bdgenomics/cannoli/Vep.scala b/core/src/main/scala/org/bdgenomics/cannoli/Vep.scala index df1ee70..87c2597 100644 --- a/core/src/main/scala/org/bdgenomics/cannoli/Vep.scala +++ b/core/src/main/scala/org/bdgenomics/cannoli/Vep.scala @@ -83,12 +83,11 @@ class Vep( .setExecutable(args.executable) .add("--format") .add("vcf") + .add("--vcf") .add("--output_file") .add("STDOUT") - .add("--vcf_info_field") - .add("ANN") .add("--terms") - .add("so") + .add("SO") .add("--no_stats") .add("--offline") .add("--dir_cache")