diff --git a/snakePipes/parserCommon.py b/snakePipes/parserCommon.py
index 0042ce5da..cf0280d43 100644
--- a/snakePipes/parserCommon.py
+++ b/snakePipes/parserCommon.py
@@ -168,7 +168,8 @@ def snpArguments(defaults):
 
     snpargs.add_argument("--NMaskedIndex",
                          default='',
-                         help="N-masked index of the reference genome (default: 'None')")
+                         help="N-masked index of the reference genome (default: 'None'). "
+                         "Note that this should point to a file (i.e. 'Genome' for STAR indices, genome.1.bt2 for bowtie2 indices).")
 
     return parser
 
diff --git a/snakePipes/shared/rules/SNPsplit.snakefile b/snakePipes/shared/rules/SNPsplit.snakefile
index 37169ab55..ea06f0f15 100644
--- a/snakePipes/shared/rules/SNPsplit.snakefile
+++ b/snakePipes/shared/rules/SNPsplit.snakefile
@@ -8,8 +8,8 @@ if aligner == "Bowtie2":
         output:
             targetbam = expand("allelic_bams/{{sample}}.filtered.{suffix}.bam", suffix = ['allele_flagged', 'genome1', 'genome2', 'unassigned']),
             tempbam = temp("filtered_bam/{sample}.filtered.sortedByName.bam"),
-            rep1 = "allelic_bams/{sample}.SNPsplit_report.yaml",
-            rep2 = "allelic_bams/{sample}.SNPsplit_sort.yaml"
+            rep1 = "allelic_bams/{sample}.filtered.SNPsplit_report.yaml",
+            rep2 = "allelic_bams/{sample}.filtered.SNPsplit_sort.yaml"
         log: "allelic_bams/logs/{sample}.snp_split.log"
         params:
             pairedEnd = '--paired' if pairedEnd else '',
diff --git a/snakePipes/shared/rules/multiQC.snakefile b/snakePipes/shared/rules/multiQC.snakefile
index 619a05398..308cbc060 100755
--- a/snakePipes/shared/rules/multiQC.snakefile
+++ b/snakePipes/shared/rules/multiQC.snakefile
@@ -61,8 +61,8 @@ def multiqc_input_check(return_value):
                 infiles.append( expand("Qualimap_qc/{sample}.filtered.bamqc_results.txt", sample = samples) )
                 indir += " Qualimap_qc "
         if "allelic-mapping" in mode:
-            infiles.append( expand("allelic_bams/{sample}.SNPsplit_report.yaml", sample = samples) )
-            infiles.append( expand("allelic_bams/{sample}.SNPsplit_sort.yaml", sample = samples) )
+            infiles.append( expand("allelic_bams/{sample}.filtered.SNPsplit_report.yaml", sample = samples) )
+            infiles.append( expand("allelic_bams/{sample}.filtered.SNPsplit_sort.yaml", sample = samples) )
             indir += "allelic_bams"
     elif pipeline=="rna-seq":
         # must be RNA-mapping, add files as per the mode