diff --git a/README.rst b/README.rst
index 4ddea58..a19c837 100644
--- a/README.rst
+++ b/README.rst
@@ -164,6 +164,12 @@ Re-label events with probability >= 0.3 as PASS::
 
     dysgu filter --pass-prob 0.3 input.vcf > output.vcf
 
+Use normal bams to filter common/germline structural variants::
+
+    dysgu filter input.vcf normal.bam > output.vcf
+    dysgu filter input.vcf normals/*.bam > output.vcf
+    dysgu filter input.vcf list_of_normals.txt > output.vcf
+
 
 ➕ Merging SVs
 --------------
@@ -201,6 +207,7 @@ cohort SVs can be merged using `dysgu merge`, before filtering to get unique SVs
 
     dysgu merge *.vcf > merged.vcf
     dysgu filter --normal-vcf merged.vcf sample1.vcf *.bam > sample1_unique.vcf
+    dysgu filter --normal-vcf merged.vcf sample1.vcf list_of_normals.txt > sample1_unique.vcf
 
 Here, sample1.vcf and merged.vcf can contain multiple samples, although if sample1.vcf is multi-sample, you must provide '--target-sample' to indicate which sample to filter.
 The output sample1_somatic.vcf will be a single sample vcf containing unique SVs.
diff --git a/dysgu/main.py b/dysgu/main.py
index 6714c90..bf328ab 100644
--- a/dysgu/main.py
+++ b/dysgu/main.py
@@ -245,7 +245,7 @@ def run_pipeline(ctx, **kwargs):
     dest = os.path.expanduser(kwargs["working_directory"])
     logging.info(f"Destination: {dest}")
     bname = os.path.splitext(os.path.basename(kwargs["bam"]))[0]
-    tmp_file_name = f"{dest}/{bname if bname != '-' else dest}.{pfix}.bam"
+    tmp_file_name = f"{dest}/{bname if bname != '-' else os.path.basename(kwargs['working_directory'])}.{pfix}.bam"
     ctx.obj["output"] = tmp_file_name
     ctx.obj["reads"] = "None"
     max_cov_value = sv2bam.process(ctx.obj)
diff --git a/setup.py b/setup.py
index 1fa3e74..1e87c30 100644
--- a/setup.py
+++ b/setup.py
@@ -164,7 +164,7 @@ def get_extra_args():
     url="https://github.com/kcleal/dysgu",
     description="Structural variant calling",
     license="MIT",
-    version='1.6.1',
+    version='1.6.2',
     python_requires='>=3.7',
     install_requires=[  # runtime requires
             'setuptools>=63.0',