diff --git a/snakePipes/shared/rules/whatshap.snakefile b/snakePipes/shared/rules/whatshap.snakefile
index 261bb0945..b41e79eef 100644
--- a/snakePipes/shared/rules/whatshap.snakefile
+++ b/snakePipes/shared/rules/whatshap.snakefile
@@ -5,8 +5,8 @@ rule whatshap_haplotag:
             bam = "filtered_bam/{sample}.filtered.bam",
             bai = "filtered_bam/{sample}.filtered.bam.bai"
         output:
-            hbam = "allelic_bams/{sample}.filtered.allele_flagged.sorted.bam",
-            hlist = "allelic_bams/{sample}.filtered_haplotype_list.tsv"
+            hbam = "allelic_bams/{sample}.allele_flagged.sorted.bam",
+            hlist = "allelic_bams/{sample}_haplotype_list.tsv"
         benchmark:
             "allelic_bams/.benchmark/whatshap_haplotag.{sample}.benchmark"
         threads: 4
@@ -17,12 +17,12 @@ rule whatshap_haplotag:
 
 rule whatshap_split:
         input:
-            hbam = "allelic_bams/{sample}.filtered.allele_flagged.sorted.bam",
-            hlist = "allelic_bams/{sample}.filtered_haplotype_list.tsv"
+            hbam = "allelic_bams/{sample}.allele_flagged.sorted.bam",
+            hlist = "allelic_bams/{sample}_haplotype_list.tsv"
         output:
-            h1bam = "allelic_bams/{sample}.filtered.genome1.sorted.bam",
-            h2bam = "allelic_bams/{sample}.filtered.genome2.sorted.bam",
-            unbam = "allelic_bams/{sample}.filtered.unassigned.sorted.bam"
+            h1bam = "allelic_bams/{sample}.genome1.sorted.bam",
+            h2bam = "allelic_bams/{sample}.genome2.sorted.bam",
+            unbam = "allelic_bams/{sample}.unassigned.sorted.bam"
         benchmark:
             "allelic_bams/.benchmark/whatshap_split.{sample}.benchmark"
         conda: CONDA_WHATSHAP_ENV