diff --git a/tests/resources/expected_out/test_files_shortened.vcf b/tests/resources/expected_out/test_files_shortened.vcf
deleted file mode 100644
index b867dc6..0000000
--- a/tests/resources/expected_out/test_files_shortened.vcf
+++ /dev/null
@@ -1,17 +0,0 @@
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-##source=SHAPEIT2.v837
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-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Gambian	Chinese	French	Brazilian	Nigerian	Pakistani	English	Colombian	Indian	Japanese
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-1	846854	rs111957712	G	A	100	.	AC=114;AN=5008;DP=20538	GT	./.	0|0	0|0	0|0	0|0	0|0	./.	./.	0|0	0|0
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-1	847228	rs3905286	C	T	100	.	AC=1215;AN=5008;DP=20731	GT	1|1	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|1	0|0
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-1	848445	rs4626817	G	A	100	.	AC=1255;AN=5008;DP=18444	GT	1|1	0|0	0|0	0|0	0|0	0|0	0|0	./.	./.	0|0
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-1	848738	rs3829741	C	T	100	.	AC=855;AN=5008;DP=16663	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|1	0|0
diff --git a/tests/resources/test_files_shortened_haploid.vcf b/tests/resources/test_files_shortened_haploid.vcf
new file mode 100644
index 0000000..4c526fd
--- /dev/null
+++ b/tests/resources/test_files_shortened_haploid.vcf
@@ -0,0 +1,17 @@
+##fileformat=VCFv4.1
+##fileDate=10122015_22h01m13s
+##source=SHAPEIT2.v837
+##log_file=shapeit_10122015_22h01m13s_3f764d75-2fbb-42df-ab75-8c2dfd5731ce.log
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Phased Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Gambian	Chinese	French	Brazilian	Nigerian	Pakistani	English	Colombian	Indian	Japanese
+1	846808	rs4475691	C	T	100	.	AC=1276;AN=5008;DP=20368	GT:GQ:DP	1:70:60	0:30:10	0:20:40	./.:0:0	0:70:60	0:90:30	0:80:70	0:50:80	./.:0:0	0:100:80	
+1	846854	rs111957712	G	A	100	.	AC=114;AN=5008;DP=20538	GT:GQ:DP	./.:0:0	0:40:30	0:80:30	0:0:20	0:40:80	0:10:30	./.:0:0	./.:0:0	0:70:0	0:90:30	
+1	846864	rs950122	G	C	100	.	AC=1116;AN=5008;DP=20582	GT:GQ:DP	1:60:0	0:20:0	0:90:70	0:80:50	0:80:30	0:10:80	0:100:20	0:30:40	./.:0:0	0:30:90	
+1	847228	rs3905286	C	T	100	.	AC=1215;AN=5008;DP=20731	GT:GQ:DP	1:70:80	0:90:80	0:60:50	0:60:90	0:30:40	0:70:10	0:100:80	0:100:50	0:70:100	0:40:40	
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+1	848445	rs4626817	G	A	100	.	AC=1255;AN=5008;DP=18444	GT:GQ:DP	1:100:40	0:80:90	0:30:100	0:100:60	0:40:90	0:20:30	0:70:100	./.:0:0	./.:0:0	0:80:30	
+1	848456	rs11507767	A	G	100	.	AC=1266;AN=5008;DP=18137	GT:GQ:DP	1:40:30	./.:0:0	0:60:90	0:60:40	0:100:80	0:50:50	0:0:10	0:60:0	0:100:100	./.:0:0 
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