diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index 63803f26ed99a113f5d87b4f0c8609c4212f75d2..82526e7fca343a413933432beed7fa6e87193ef4 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -125,6 +125,10 @@ process recalibrate_snp_table {
   script:
   xmx_memory = "${task.memory}" - ~/\s*GB/
 """
+gatk --java-options "-Xmx${xmx_memory}G" IndexFeatureFile \
+  -I ${snp_file}
+gatk --java-options "-Xmx${xmx_memory}G" IndexFeatureFile \
+  -I ${indel_file}
 gatk --java-options "-Xmx${xmx_memory}G" BaseRecalibrator \
   -R ${fasta} \
   -I ${bam} \