From 5684640d81e720599a4200fbd8649ab4924e5fcb Mon Sep 17 00:00:00 2001 From: Dominika Maziec Date: Mon, 12 Oct 2020 09:38:08 +0200 Subject: [PATCH] Vep vcf output format --- core/src/main/scala/org/bdgenomics/cannoli/Vep.scala | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/core/src/main/scala/org/bdgenomics/cannoli/Vep.scala b/core/src/main/scala/org/bdgenomics/cannoli/Vep.scala index df1ee70e..87c25976 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")