diff --git a/strkit/call/call_sample.py b/strkit/call/call_sample.py
index 4bb3ab3..6c222e2 100644
--- a/strkit/call/call_sample.py
+++ b/strkit/call/call_sample.py
@@ -317,7 +317,7 @@ def call_sample(
 
             #  - write partial results to VCF if we're writing a VCF
             if vf is not None:
-                output_vcf_lines(params, sample_id_str, vf, results)
+                output_vcf_lines(params, sample_id_str, vf, results, logger)
 
             last_qsize = qsize
             qsize = locus_queue.qsize()
diff --git a/strkit/call/output/vcf.py b/strkit/call/output/vcf.py
index 6b23ff4..261c692 100644
--- a/strkit/call/output/vcf.py
+++ b/strkit/call/output/vcf.py
@@ -1,4 +1,5 @@
 import functools
+import logging
 import pathlib
 import pysam
 from os.path import commonprefix
@@ -84,6 +85,7 @@ def output_vcf_lines(
     sample_id: str,
     variant_file: pysam.VariantFile,
     results: tuple[dict, ...],
+    logger: logging.Logger,
 ):
     contig_vrs: list[pysam.VariantRecord] = []
 
@@ -166,6 +168,10 @@ def _write_contig_vrs():
                 snv_alleles = (ref, *snv_alts)
                 snv_pos = snv["pos"]
 
+                if len(snv_alleles) < 2:
+                    logger.error(f"Error while writing VCF: SNV ({snv_id}) at {contig}:{snv_pos+1} has no alts")
+                    continue
+
                 snv_vr = variant_file.new_record(
                     contig=contig,
                     id=snv_id,