From 9da85209f234e10d8e84b11d9bd7ee39a2a2fc4f Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 22 Apr 2022 11:05:56 +0200
Subject: [PATCH] change bcftools output format

---
 conf/pipeline/raredisease/hasta.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config
index 18c7bab..1359522 100644
--- a/conf/pipeline/raredisease/hasta.config
+++ b/conf/pipeline/raredisease/hasta.config
@@ -15,9 +15,9 @@ process {
     }
     withName: BCFTOOLS_VIEW {
         if (params.genome == 'GRCh37') {
-            ext.args = '--output-type v --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "'
+            ext.args = '--output-type z --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "'
         } else if (params.genome == 'GRCh38') {
-            ext.args = '--output-type v --apply-filters PASS --exclude "INFO/swegen_FRQ > 0.40"'
+            ext.args = '--output-type z --apply-filters PASS --exclude "INFO/swegen_FRQ > 0.40"'
         }
         publishDir = [
             enabled: false,