diff --git a/src/.docker_modules/bwa/0.7.17/Dockerfile b/src/.docker_modules/bwa/0.7.17/Dockerfile
index 0e55612184dd340e5992f850088203c0240bde23..eaae571bccea25e5f9938667009f7d3a1290b48f 100644
--- a/src/.docker_modules/bwa/0.7.17/Dockerfile
+++ b/src/.docker_modules/bwa/0.7.17/Dockerfile
@@ -1,4 +1,4 @@
-FROM lbmc/sambamba:0.6.9
+FROM lbmc/samtools:1.11
 MAINTAINER Laurent Modolo
 
 ENV BWA_VERSION=0.7.17
diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index 38b925128bac786698dd3f8590a3cc50ef996dcd..ada553fe2a39ef2952c04f11fe45fc6c717a4e96 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -39,7 +39,8 @@ process mapping_fastq {
 bwa mem -t ${task.cpus} \
 ${index_id} ${reads[0]} ${reads[1]} 2> \
   ${file_id}_bwa_report.txt | \
-  sambamba view -S -t ${task.cpus} -f bam - > ${file_id}.bam
+  samtools view -S -t ${task.cpus} -f bam - > ${file_id}.bam
+  samtools view -@ ${task.cpus} -Sb - > ${pair_id}.bam
 """
 }