diff --git a/conf/modules/qc.config b/conf/modules/qc.config
index 228920e3..2966216b 100644
--- a/conf/modules/qc.config
+++ b/conf/modules/qc.config
@@ -55,7 +55,13 @@ process {
     }
 
     withName: MOSDEPTH {
-        ext.args = "--by 500 --no-per-base"
+
+        // If pipeline is run with bed-file, then don't run wth '--by 500'
+        if(params.bed) {
+            ext.args = "--no-per-base"
+        } else {
+            ext.args = "--by 500 --no-per-base"
+        }
 
         publishDir = [
             path: { "${params.outdir}/qc/mosdepth/${meta.id}" },
diff --git a/subworkflows/local/qc_aligned_reads.nf b/subworkflows/local/qc_aligned_reads.nf
index 343cd1ec..74be1adf 100644
--- a/subworkflows/local/qc_aligned_reads.nf
+++ b/subworkflows/local/qc_aligned_reads.nf
@@ -4,26 +4,22 @@ include { MOSDEPTH } from '../../modules/nf-core/mosdepth/main.nf'
 workflow QC_ALIGNED_READS {
 
     take:
-    ch_bam   // channel: [ val(meta), bam ]
-    ch_bai   // channel: [ val(meta), bai ]
-    ch_fasta // channel: [ val(meta), fasta ]
+    ch_bam_bai // channel: [ val(meta), [bam, bai] ]
+    ch_fasta   // channel: [ val(meta), fasta ]
+    ch_bed     // channel: [ val(meta), bed ]
 
     main:
     ch_versions = Channel.empty()
 
     // Prepare inputs
-    ch_bam
-        .join(ch_bai)
-        .set{ ch_cramino_in }
-    
-    // Prepare inputs
-    ch_cramino_in
-        .map{ meta, bam, bai -> [ meta, bam, bai, [] ] }
-        .set{ ch_mosdepth_in }   
-    
-    CRAMINO (ch_cramino_in)
+    ch_bam_bai
+        .combine(ch_bed.map{ meta, bed -> bed })
+        //.map{ meta, bam, bai -> [ meta, bam, bai, [] ] }
+        .set{ ch_mosdepth_in }
+
+    CRAMINO (ch_bam_bai)
     MOSDEPTH(ch_mosdepth_in, ch_fasta)
-    
+
     // Gather versions
     ch_versions = ch_versions.mix(CRAMINO.out.versions.first())
     ch_versions = ch_versions.mix(MOSDEPTH.out.versions.first())
diff --git a/workflows/skierfe.nf b/workflows/skierfe.nf
index 48568c17..e224551a 100644
--- a/workflows/skierfe.nf
+++ b/workflows/skierfe.nf
@@ -40,6 +40,7 @@ ch_extra_snfs     = params.extra_snfs     ? Channel.fromSamplesheet('extra_snfs'
 ch_extra_gvcfs    = params.extra_gvcfs    ? Channel.fromSamplesheet('extra_gvcfs', immutable_meta: false)           : Channel.empty()
 ch_tandem_repeats = params.tandem_repeats ? Channel.fromPath(params.tandem_repeats).collect()                       : Channel.value([])
 ch_bed            = params.bed            ? Channel.fromPath(params.bed).map{ [ it.getSimpleName(), it]}.collect()  : Channel.empty()
+ch_input_bed            = params.bed            ? Channel.fromPath(params.bed).map{ [ it.getSimpleName(), it]}.collect()  : Channel.value([])
 
 // This should be able to in schema?
 if (params.split_fastq < 250 & params.split_fastq > 0 ) { exit 1, '--split_fastq must be 0 or >= 250'}
@@ -241,7 +242,7 @@ workflow SKIERFE {
                     .flatten())
             .set{ ch_snv_calling_in }
 
-        QC_ALIGNED_READS( bam, bai, fasta )
+        QC_ALIGNED_READS( bam_bai, fasta, ch_input_bed )
 
         // Call SVs with Sniffles2
         STRUCTURAL_VARIANT_CALLING( bam_bai , ch_extra_snfs, fasta, fai, ch_tandem_repeats )