gatk4: fix option for Haplotypecaller

3ea4e9e6 · Laurent Modolo · 913a420c · 3ea4e9e6
Verified Commit 3ea4e9e6 authored 4 years ago by Laurent Modolo
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -176,7 +176,6 @@ gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCaller \
  -R ${fasta} \
  -I ${bam} \
  -ERC GVCF \
-  -variant_index_type LINEAR -variant_index_parameter 128000 \
  -O ${file_id}.gvcf
 """
 }