diff --git a/CHANGELOG.md b/CHANGELOG.md
index 49943ad938..106c24c75d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -142,6 +142,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#641](https://github.com/nf-core/sarek/pull/641) - Fix issue with duplicate substring in tools and skip_tools
 - [#642](https://github.com/nf-core/sarek/pull/642) - Only unzip ref files if tool is run, only publish ref files if `--save_reference` and simplify CNKit logic
 - [#650](https://github.com/nf-core/sarek/pull/650) - Fix intervals checks
+- [#654](https://github.com/nf-core/sarek/pull/654) - Allow any step but annotation to start from BAM files
 
 ### Deprecated
 
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
index b915f192cb..82a3d8fdb4 100644
--- a/workflows/sarek.nf
+++ b/workflows/sarek.nf
@@ -1154,9 +1154,9 @@ def extract_csv(csv_file) {
 
             meta.size       = 1 // default number of splitted fastq
 
-            if (params.step == 'mapping') return [meta, bam, bai]
+            if (params.step != 'annotate') return [meta, bam, bai]
             else {
-                log.error "Samplesheet contains ubam files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations"
+                log.error "Samplesheet contains bam files but step is `annotate`. The pipeline is expecting vcf files for the annotation. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations"
                 System.exit(1)
             }