diff --git a/CHANGELOG.md b/CHANGELOG.md
index 09fec65b7..c95c21f1a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Fixed`
 
+- [#824](https://github.com/nf-core/eager/issues/824) Fixes large memory footprint of bedtools coverage calculation.
 - [#822](https://github.com/nf-core/eager/issues/822) Fixed post-adapterremoval trimmed files not being lane-merged and included in downstream analyses
 
 ### `Dependencies`
diff --git a/main.nf b/main.nf
index 4683d8238..65813086f 100644
--- a/main.nf
+++ b/main.nf
@@ -2054,8 +2054,12 @@ process bedtools {
 
   script:
   """
-  bedtools coverage -nonamecheck -a ${anno_file} -b $bam | pigz -p ${task.cpus - 1} > "${bam.baseName}".breadth.gz
-  bedtools coverage -nonamecheck -a ${anno_file} -b $bam -mean | pigz -p ${task.cpus - 1} > "${bam.baseName}".depth.gz
+  ## Create genome file from bam header
+  samtools view -H ${bam} | grep '@SQ' | sed 's#@SQ\tSN:\\|LN:##g' > genome.txt
+  
+  ##  Run bedtools
+  bedtools coverage -nonamecheck -g genome.txt -sorted -a ${anno_file} -b ${bam} | pigz -p ${task.cpus - 1} > "${bam.baseName}".breadth.gz
+  bedtools coverage -nonamecheck -g genome.txt -sorted -a ${anno_file} -b ${bam} -mean | pigz -p ${task.cpus - 1} > "${bam.baseName}".depth.gz
   """
 }