Make --merge both and --merge none work with indel-only records

pd3 · pd3 · commit a35ad84fd684 · 2025-02-18T11:01:54.000Z
The code was making the incorrect assumption of always having a SNP record available. However, that is not always the case and prevents the merging of G>GT,T with G>GT. This change reorders the output lines so that indels can come first, depending on the order of files on the command line. Hopefully resolves #2339
diff --git a/NEWS b/NEWS
@@ -39,6 +39,9 @@ Changes affecting specific commands:
     - The option `--merge none` is expected to create no new multiallelic sites, but it should
       allow to merge, say, A>C with A>C,AT (#2333)
 
+    - Make `--merge both` work with indel-only records; for example, the multiallelic
+      site G>GT,T should be merged with G>GT (#2339)
+
 * bcftools norm
 
     - Print the number of removed duplicate sites in the final statistics (#2346)
diff --git a/test/merge.2.both.out b/test/merge.2.both.out
@@ -21,12 +21,12 @@
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B	2:A	2:B
-1	3000000	.	C	G	59.2	PASS	AN=4;AC=2	GT:GQ	./.:.	./.:.	0/1:245	0/1:245
 1	3000000	.	C	CCG	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245	./.:.	./.:.
+1	3000000	.	C	G	59.2	PASS	AN=4;AC=2	GT:GQ	./.:.	./.:.	0/1:245	0/1:245
 1	3000150	.	C	A,G	59.2	PASS	AN=8;AC=2,2	GT:GQ	0/1:245	0/1:245	0/2:245	0/2:245
 1	3000151	.	C	A,G	59.2	PASS	AN=8;AC=2,2	GT:DP:GQ	0/1:32:245	0/1:32:245	0/2:32:245	0/2:32:245
-1	3106154	.	C	A,T	59.2	PASS	AN=8;AC=2,2	GT:GQ:DP	0/1:245:32	0/1:245:32	0/2:245:32	0/2:245:32
 1	3106154	.	C	CC,CCC	342	PASS	AN=8;AC=2,2	GT:GQ:DP	0/1:245:32	0/1:245:32	0/2:245:32	0/2:245:32
+1	3106154	.	C	A,T	59.2	PASS	AN=8;AC=2,2	GT:GQ:DP	0/1:245:32	0/1:245:32	0/2:245:32	0/2:245:32
 1	3200000	.	C	T	59.2	PASS	AN=8;AC=4	GT:GQ:DP	0/1:245:32	0/1:245:32	0/1:245:32	0/1:245:32
 1	3200010	.	C	T,A	59.2	PASS	AN=8;AC=2,2	GT:GQ:DP	0/1:245:32	0/1:245:32	0/2:245:32	0/2:245:32
 1	3200020	.	C	G,T	59.2	PASS	AN=0;AC=0,0	GT:GL	./.:1,2,3,4,5,6	.:1,2,3	./.:1,2,3,4,5,6	.:1,2,3
diff --git a/test/merge.2.none.out b/test/merge.2.none.out
@@ -21,16 +21,16 @@
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B	2:A	2:B
-1	3000000	.	C	G	59.2	PASS	AN=4;AC=2	GT:GQ	./.:.	./.:.	0/1:245	0/1:245
 1	3000000	.	C	CCG	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245	./.:.	./.:.
+1	3000000	.	C	G	59.2	PASS	AN=4;AC=2	GT:GQ	./.:.	./.:.	0/1:245	0/1:245
 1	3000150	.	C	A	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245	./.:.	./.:.
 1	3000150	.	C	G	59.2	PASS	AN=4;AC=2	GT:GQ	./.:.	./.:.	0/1:245	0/1:245
 1	3000151	.	C	A	59.2	PASS	AN=4;AC=2	GT:DP:GQ	0/1:32:245	0/1:32:245	./.:.:.	./.:.:.
 1	3000151	.	C	G	59.2	PASS	AN=4;AC=2	GT:DP:GQ	./.:.:.	./.:.:.	0/1:32:245	0/1:32:245
-1	3106154	.	C	A	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32	./.:.:.	./.:.:.
-1	3106154	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	./.:.:.	./.:.:.	0/1:245:32	0/1:245:32
 1	3106154	.	C	CC	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32	./.:.:.	./.:.:.
+1	3106154	.	C	A	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32	./.:.:.	./.:.:.
 1	3106154	.	C	CCC	342	PASS	AN=4;AC=2	GT:GQ:DP	./.:.:.	./.:.:.	0/1:245:32	0/1:245:32
+1	3106154	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	./.:.:.	./.:.:.	0/1:245:32	0/1:245:32
 1	3200000	.	C	T	59.2	PASS	AN=8;AC=4	GT:GQ:DP	0/1:245:32	0/1:245:32	0/1:245:32	0/1:245:32
 1	3200010	.	C	T,A	59.2	PASS	AN=8;AC=2,2	GT:GQ:DP	0/1:245:32	0/1:245:32	0/2:245:32	0/2:245:32
 1	3200020	.	C	G,T	59.2	PASS	AN=0;AC=0,0	GT:GL	./.:1,2,3,4,5,6	.:1,2,3	./.:1,2,3,4,5,6	.:1,2,3
diff --git a/test/merge.abc.2.out b/test/merge.abc.2.out
@@ -38,14 +38,14 @@
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B	2:B	C	D
 1	3000150	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245	./.:.	./.:.	./.:.
 1	3000151	.	C	T	59.2	PASS	AN=4;AC=2	GT:DP:GQ	0/1:32:245	0/1:32:245	./.:.:.	./.:.:.	./.:.:.
-1	3062915	idSNP	G	T,C,A	419	test;q20	TEST=5;STR=.;DP=14;DP4=3,6,9,12;INTA=2,1,.;AN=9;AC=2,2,1	GT:TT:GQ:DP:GL:STR	0/1:0,1,.:409:35:-20,-5,-20,-20,-5,-20,.,.,.,.:.	2:0,1,.:409:35:-20,-5,-20,.:.	0/3:.:376:14:-10,.,.,.,.,.,0,.,.,-10:ABC	0/2:1,0,.:409:35:-20,-20,-20,-5,-5,-20,.,.,.,.:.	0/1:1,0,.:409:35:-20,-20,-20,-5,-5,-20,.,.,.,.:.
 1	3062915	id3D	GTTT	G	84.6	q10;q20	INDEL;STR=test;TXT=AA;DP=1013;DP4=6,7,8,9;AN=10;AC=5	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20	0/1:376:14:-10,0,-10	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20
+1	3062915	idSNP	G	T,C,A	419	test;q20	TEST=5;STR=.;DP=14;DP4=3,6,9,12;INTA=2,1,.;AN=9;AC=2,2,1	GT:TT:GQ:DP:GL:STR	0/1:0,1,.:409:35:-20,-5,-20,-20,-5,-20,.,.,.,.:.	2:0,1,.:409:35:-20,-5,-20,.:.	0/3:.:376:14:-10,.,.,.,.,.,0,.,.,-10:ABC	0/2:1,0,.:409:35:-20,-20,-20,-5,-5,-20,.,.,.,.:.	0/1:1,0,.:409:35:-20,-20,-20,-5,-5,-20,.,.,.,.:.
 1	3062915	id1D;id2D	GTT	GT,G	999	q20;q10	DP=14;DP4=2,4,6,8;AN=6;AC=1,2	GT:GQ:DP:GL:STR	./.:.:.:.:.	./.:.:.:.:.	0/1:376:14:-10,0,-10,.,.,.:DEF	0/2:409:35:-20,.,.,-5,.,-20:.	0/2:409:35:-20,.,.,-5,.,-20:.
-1	3106154	.	C	T	999	PASS	DP=15;AN=2;AC=1	GT:GQ:DP:GL	./.:.:.:.	./.:.:.:.	0/1:277:15:-10,0,-10	./.:.:.:.	./.:.:.:.
 1	3106154	.	CAAAA	CA,C	342	PASS	DP=15;AN=6;AC=2,1	GT:GQ:DP:GL	0/1:245:32:.	0/1:245:32:.	0/2:277:15:-10,.,.,0,.,-10	.:245:32:.	./.:245:32:.
 1	3106154	.	C	CT	459	PASS	AN=8;AC=4	GT:GQ:DP	0/1:245:32	0/1:245:32	./.:.:.	0/1:245:32	0/1:245:32
-1	3157410	.	G	T	46.7	q10	AN=4;AC=4	GT:GQ:DP	./.:.:.	./.:.:.	./.:.:.	1/1:21:21	1/1:21:21
+1	3106154	.	C	T	999	PASS	DP=15;AN=2;AC=1	GT:GQ:DP:GL	./.:.:.:.	./.:.:.:.	0/1:277:15:-10,0,-10	./.:.:.:.	./.:.:.:.
 1	3157410	.	GAC	GC,G	90.6	PASS	DP=11;AN=6;AC=4,1	GT:GQ:DP	1/1:21:21	1/1:21:21	0/2:49:11	./.:.:.	./.:.:.
+1	3157410	.	G	T	46.7	q10	AN=4;AC=4	GT:GQ:DP	./.:.:.	./.:.:.	./.:.:.	1/1:21:21	1/1:21:21
 1	3162006	.	GAA	G,GA	238	PASS	DP=19;XRF=1e+06,2e+06,500000;XRI=1111,2222,5555;XRS=AAA,BBB,DDD;XAF=1e+06,500000;XAI=1111,5555;XAS=AAA,DDD;XGF=1e+06,2e+06,3e+06,500000,.,9e+09;XGI=1111,2222,3333,5555,.,9999;XGS=A,B,C,E,.,F;AN=10;AC=3,2	GT:GQ:DP	0/1:212:22	0/1:212:22	0/1:589:19	0/2:212:22	0/2:212:22
 1	3177144	.	G	T	999	PASS	DP=24;AN=10;AC=3	GT:GQ:DP	0/0:150:30	1/1:150:30	0/1:236:24	0/0:150:30	0/0:150:30
 1	3177144	.	GT	G	999	PASS	DP=24;AN=6;AC=1	GT:GQ:DP	0/0:150:30	0/0:150:30	0/1:236:24	./.:.:.	./.:.:.
diff --git a/test/merge.abc.3.out b/test/merge.abc.3.out
@@ -38,14 +38,14 @@
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B	2:B	C	D
 1	3000150	.	C	T	59.2	PASS	AN=10;AC=2	GT:GQ	0/1:245	0/1:245	0/0:.	0/0:.	0/0:.
 1	3000151	.	C	T	59.2	PASS	AN=10;AC=2	GT:DP:GQ	0/1:32:245	0/1:32:245	0/0:.:.	0/0:.:.	0/0:.:.
-1	3062915	idSNP	G	T,C,A	419	test;q20	TEST=5;STR=.;DP=14;DP4=3,6,9,12;INTA=2,1,.;AN=9;AC=2,2,1	GT:TT:GQ:DP:GL:STR	0/1:0,1,.:409:35:-20,-5,-20,-20,-5,-20,.,.,.,.:.	2:0,1,.:409:35:-20,-5,-20,.:.	0/3:.:376:14:-10,.,.,.,.,.,0,.,.,-10:ABC	0/2:1,0,.:409:35:-20,-20,-20,-5,-5,-20,.,.,.,.:.	0/1:1,0,.:409:35:-20,-20,-20,-5,-5,-20,.,.,.,.:.
 1	3062915	id3D	GTTT	G	84.6	q10;q20	INDEL;STR=test;TXT=AA;DP=1013;DP4=6,7,8,9;AN=10;AC=5	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20	0/1:376:14:-10,0,-10	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20
+1	3062915	idSNP	G	T,C,A	419	test;q20	TEST=5;STR=.;DP=14;DP4=3,6,9,12;INTA=2,1,.;AN=9;AC=2,2,1	GT:TT:GQ:DP:GL:STR	0/1:0,1,.:409:35:-20,-5,-20,-20,-5,-20,.,.,.,.:.	2:0,1,.:409:35:-20,-5,-20,.:.	0/3:.:376:14:-10,.,.,.,.,.,0,.,.,-10:ABC	0/2:1,0,.:409:35:-20,-20,-20,-5,-5,-20,.,.,.,.:.	0/1:1,0,.:409:35:-20,-20,-20,-5,-5,-20,.,.,.,.:.
 1	3062915	id1D;id2D	GTT	GT,G	999	q20;q10	DP=14;DP4=2,4,6,8;AN=10;AC=1,2	GT:GQ:DP:GL:STR	0/0:.:.:.:.	0/0:.:.:.:.	0/1:376:14:-10,0,-10,.,.,.:DEF	0/2:409:35:-20,.,.,-5,.,-20:.	0/2:409:35:-20,.,.,-5,.,-20:.
-1	3106154	.	C	T	999	PASS	DP=15;AN=10;AC=1	GT:GQ:DP:GL	0/0:.:.:.	0/0:.:.:.	0/1:277:15:-10,0,-10	0/0:.:.:.	0/0:.:.:.
 1	3106154	.	CAAAA	CA,C	342	PASS	DP=15;AN=6;AC=2,1	GT:GQ:DP:GL	0/1:245:32:.	0/1:245:32:.	0/2:277:15:-10,.,.,0,.,-10	.:245:32:.	./.:245:32:.
 1	3106154	.	C	CT	459	PASS	AN=10;AC=4	GT:GQ:DP	0/1:245:32	0/1:245:32	0/0:.:.	0/1:245:32	0/1:245:32
-1	3157410	.	G	T	46.7	q10	AN=10;AC=4	GT:GQ:DP	0/0:.:.	0/0:.:.	0/0:.:.	1/1:21:21	1/1:21:21
+1	3106154	.	C	T	999	PASS	DP=15;AN=10;AC=1	GT:GQ:DP:GL	0/0:.:.:.	0/0:.:.:.	0/1:277:15:-10,0,-10	0/0:.:.:.	0/0:.:.:.
 1	3157410	.	GAC	GC,G	90.6	q10	DP=11;AN=10;AC=4,1	GT:GQ:DP	1/1:21:21	1/1:21:21	0/2:49:11	0/0:.:.	0/0:.:.
+1	3157410	.	G	T	46.7	q10	AN=10;AC=4	GT:GQ:DP	0/0:.:.	0/0:.:.	0/0:.:.	1/1:21:21	1/1:21:21
 1	3162006	.	GAA	G,GA	238	PASS	DP=19;XRF=1e+06,2e+06,500000;XRI=1111,2222,5555;XRS=AAA,BBB,DDD;XAF=1e+06,500000;XAI=1111,5555;XAS=AAA,DDD;XGF=1e+06,2e+06,3e+06,500000,.,9e+09;XGI=1111,2222,3333,5555,.,9999;XGS=A,B,C,E,.,F;AN=10;AC=3,2	GT:GQ:DP	0/1:212:22	0/1:212:22	0/1:589:19	0/2:212:22	0/2:212:22
 1	3177144	.	G	T	999	PASS	DP=24;AN=10;AC=3	GT:GQ:DP	0/0:150:30	1/1:150:30	0/1:236:24	0/0:150:30	0/0:150:30
 1	3177144	.	GT	G	999	PASS	DP=24;AN=10;AC=1	GT:GQ:DP	0/0:150:30	0/0:150:30	0/1:236:24	0/0:.:.	0/0:.:.
diff --git a/test/merge.abc.out b/test/merge.abc.out
@@ -38,14 +38,14 @@
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B	2:B	C	D
 1	3000150	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245	./.:.	./.:.	./.:.
 1	3000151	.	C	T	59.2	PASS	AN=4;AC=2	GT:DP:GQ	0/1:32:245	0/1:32:245	./.:.:.	./.:.:.	./.:.:.
-1	3062915	idSNP	G	T,C,A	419	test;q20	TEST=5;STR=.;DP=14;DP4=3,6,9,12;INTA=2,1,.;AN=9;AC=2,2,1	GT:TT:GQ:DP:GL:STR	0/1:0,1,.:409:35:-20,-5,-20,-20,-5,-20,.,.,.,.:.	2:0,1,.:409:35:-20,-5,-20,.:.	0/3:.:376:14:-10,.,.,.,.,.,0,.,.,-10:ABC	0/2:1,0,.:409:35:-20,-20,-20,-5,-5,-20,.,.,.,.:.	0/1:1,0,.:409:35:-20,-20,-20,-5,-5,-20,.,.,.,.:.
 1	3062915	id3D	GTTT	G	84.6	q10;q20	INDEL;STR=test;TXT=AA;DP=1013;DP4=6,7,8,9;AN=10;AC=5	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20	0/1:376:14:-10,0,-10	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20
+1	3062915	idSNP	G	T,C,A	419	test;q20	TEST=5;STR=.;DP=14;DP4=3,6,9,12;INTA=2,1,.;AN=9;AC=2,2,1	GT:TT:GQ:DP:GL:STR	0/1:0,1,.:409:35:-20,-5,-20,-20,-5,-20,.,.,.,.:.	2:0,1,.:409:35:-20,-5,-20,.:.	0/3:.:376:14:-10,.,.,.,.,.,0,.,.,-10:ABC	0/2:1,0,.:409:35:-20,-20,-20,-5,-5,-20,.,.,.,.:.	0/1:1,0,.:409:35:-20,-20,-20,-5,-5,-20,.,.,.,.:.
 1	3062915	id1D;id2D	GTT	GT,G	999	q20;q10	DP=14;DP4=2,4,6,8;AN=6;AC=1,2	GT:GQ:DP:GL:STR	./.:.:.:.:.	./.:.:.:.:.	0/1:376:14:-10,0,-10,.,.,.:DEF	0/2:409:35:-20,.,.,-5,.,-20:.	0/2:409:35:-20,.,.,-5,.,-20:.
-1	3106154	.	C	T	999	PASS	DP=15;AN=2;AC=1	GT:GQ:DP:GL	./.:.:.:.	./.:.:.:.	0/1:277:15:-10,0,-10	./.:.:.:.	./.:.:.:.
 1	3106154	.	CAAAA	CA,C	342	PASS	DP=15;AN=6;AC=2,1	GT:GQ:DP:GL	0/1:245:32:.	0/1:245:32:.	0/2:277:15:-10,.,.,0,.,-10	.:245:32:.	./.:245:32:.
 1	3106154	.	C	CT	459	PASS	AN=8;AC=4	GT:GQ:DP	0/1:245:32	0/1:245:32	./.:.:.	0/1:245:32	0/1:245:32
-1	3157410	.	G	T	46.7	q10	AN=4;AC=4	GT:GQ:DP	./.:.:.	./.:.:.	./.:.:.	1/1:21:21	1/1:21:21
+1	3106154	.	C	T	999	PASS	DP=15;AN=2;AC=1	GT:GQ:DP:GL	./.:.:.:.	./.:.:.:.	0/1:277:15:-10,0,-10	./.:.:.:.	./.:.:.:.
 1	3157410	.	GAC	GC,G	90.6	q10	DP=11;AN=6;AC=4,1	GT:GQ:DP	1/1:21:21	1/1:21:21	0/2:49:11	./.:.:.	./.:.:.
+1	3157410	.	G	T	46.7	q10	AN=4;AC=4	GT:GQ:DP	./.:.:.	./.:.:.	./.:.:.	1/1:21:21	1/1:21:21
 1	3162006	.	GAA	G,GA	238	PASS	DP=19;XRF=1e+06,2e+06,500000;XRI=1111,2222,5555;XRS=AAA,BBB,DDD;XAF=1e+06,500000;XAI=1111,5555;XAS=AAA,DDD;XGF=1e+06,2e+06,3e+06,500000,.,9e+09;XGI=1111,2222,3333,5555,.,9999;XGS=A,B,C,E,.,F;AN=10;AC=3,2	GT:GQ:DP	0/1:212:22	0/1:212:22	0/1:589:19	0/2:212:22	0/2:212:22
 1	3177144	.	G	T	999	PASS	DP=24;AN=10;AC=3	GT:GQ:DP	0/0:150:30	1/1:150:30	0/1:236:24	0/0:150:30	0/0:150:30
 1	3177144	.	GT	G	999	PASS	DP=24;AN=6;AC=1	GT:GQ:DP	0/0:150:30	0/0:150:30	0/1:236:24	./.:.:.	./.:.:.
diff --git a/test/merge.gvcf.2.1.out b/test/merge.gvcf.2.1.out
@@ -32,10 +32,10 @@
 4	20000975	.	C	<*>	0	.	END=20001021;MinDP=33;QS=0.75,0.25	PL:DP:DV	0,4,10:4:1	.:.:.	.:.:.
 4	20001022	.	C	<*>	0	.	END=20001070;MinDP=33;QS=1.5,0.5	PL:DP:DV	0,4,10:4:1	0,4,10:4:1	.:.:.
 4	20001071	.	T	G	0	.	QS=0.75,0.25	PL:DP:DV	0,4,10:4:1	0,4,10:4:1	.:.:.
-5	110285	.	T	C	.	.	.	PL	.	114,0,15	.
 5	110285	.	TAACCCC	T	.	.	.	PL	89,6,0	.	.
-5	1110285	.	T	C	.	.	.	PL	.	114,0,15	.
+5	110285	.	T	C	.	.	.	PL	.	114,0,15	.
 5	1110285	.	T	TAACCCC	.	.	.	PL	89,6,0	.	.
+5	1110285	.	T	C	.	.	.	PL	.	114,0,15	.
 6	600	.	T	<*>	.	.	END=609	PL	66,1,1	.	.
 6	610	.	T	<*>	.	.	.	PL	66,1,1	66,2,1	.
 6	611	.	N	<*>	.	.	END=619	PL	66,1,1	.	.
diff --git a/test/merge.gvcf.2.2.out b/test/merge.gvcf.2.2.out
@@ -32,10 +32,10 @@
 4	20000975	.	C	.	0	.	END=20001021;MinDP=33;QS=0.75	PL:DP:DV	0:4:1	.:.:.	.:.:.
 4	20001022	.	C	.	0	.	END=20001070;MinDP=33;QS=1.5	PL:DP:DV	0:4:1	0:4:1	.:.:.
 4	20001071	.	T	G	0	.	QS=0.75,0.25	PL:DP:DV	0,4,10:4:1	0,4,10:4:1	.:.:.
-5	110285	.	T	C	.	.	.	PL	.	114,0,15	.
 5	110285	.	TAACCCC	T	.	.	.	PL	89,6,0	.	.
-5	1110285	.	T	C	.	.	.	PL	.	114,0,15	.
+5	110285	.	T	C	.	.	.	PL	.	114,0,15	.
 5	1110285	.	T	TAACCCC	.	.	.	PL	89,6,0	.	.
+5	1110285	.	T	C	.	.	.	PL	.	114,0,15	.
 6	600	.	T	.	.	.	END=609	PL	66	.	.
 6	610	.	T	.	.	.	.	PL	66	66	.
 6	611	.	N	.	.	.	END=619	PL	66	.	.
diff --git a/test/merge.gvcf.2.out b/test/merge.gvcf.2.out
@@ -32,10 +32,10 @@
 4	20000975	.	C	<*>	0	.	END=20001021;MinDP=33;QS=0.75,0.25	PL:DP:DV	0,4,10:4:1	.:.:.	.:.:.
 4	20001022	.	C	<*>	0	.	END=20001070;MinDP=33;QS=1.5,0.5	PL:DP:DV	0,4,10:4:1	0,4,10:4:1	.:.:.
 4	20001071	.	T	G,<*>	0	.	QS=0.75,0.25,0	PL:DP:DV	0,4,10,20,30,40:4:1	0,4,10,35,73,113:4:1	.:.:.
-5	110285	.	T	C,<*>	.	.	.	PL	.	114,0,15,35,73,113	.
 5	110285	.	TAACCCC	T	.	.	.	PL	89,6,0	.	.
-5	1110285	.	T	C,<*>	.	.	.	PL	.	114,0,15,35,73,113	.
+5	110285	.	T	C,<*>	.	.	.	PL	.	114,0,15,35,73,113	.
 5	1110285	.	T	TAACCCC	.	.	.	PL	89,6,0	.	.
+5	1110285	.	T	C,<*>	.	.	.	PL	.	114,0,15,35,73,113	.
 6	600	.	T	<*>	.	.	END=609	PL	66,1,1	.	.
 6	610	.	T	<*>	.	.	.	PL	66,1,1	66,2,1	.
 6	611	.	N	<*>	.	.	END=619	PL	66,1,1	.	.
diff --git a/test/merge.multiallelics.1.1.out b/test/merge.multiallelics.1.1.out
@@ -0,0 +1,6 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##contig=<ID=chr21,length=248956422>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	smpl1	smpl2	smpl3	smpl4	smpl5	smpl6
+chr21	14483696	rs74584932	G	GT,T	.	.	.	GT	0/0	0/1	1/1	0|0	0|1	1|1
diff --git a/test/merge.multiallelics.1.a.vcf b/test/merge.multiallelics.1.a.vcf
@@ -0,0 +1,5 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##contig=<ID=chr21,length=248956422>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	smpl1	smpl2	smpl3
+chr21	14483696	.	G	GT,T	.	.	.	GT	0/0	0/1	1/1
diff --git a/test/merge.multiallelics.1.b.vcf b/test/merge.multiallelics.1.b.vcf
@@ -0,0 +1,5 @@
+##fileformat=VCFv4.2
+##contig=<ID=chr21>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	smpl4	smpl5	smpl6
+chr21	14483696	rs74584932	G	GT	.	.	.	GT	0|0	0|1	1|1
diff --git a/test/test.pl b/test/test.pl
@@ -61,6 +61,8 @@
 run_test(\&test_vcf_isec,$opts,in=>['isec-miss.1.1','isec-miss.1.2','isec-miss.1.3'],out=>'isec-miss.1.1.out',args=>'-R {PATH}/isec-miss.1.regs.txt -n +1');
 run_test(\&test_vcf_isec,$opts,in=>['isec-miss.2.1','isec-miss.2.2','isec-miss.2.3'],out=>'isec-miss.2.1.out',args=>'-n +1 -r 20:100,20:140,12:55,20:140,20:100');
 run_test(\&test_vcf_isec,$opts,in=>['isec-miss.2.1','isec-miss.2.2','isec-miss.2.3'],out=>'isec-miss.2.1.out',args=>'-R {PATH}/isec-miss.1.regs.txt -n +1');
+run_test(\&test_vcf_merge,$opts,in=>['merge.multiallelics.1.a','merge.multiallelics.1.b'],out=>'merge.multiallelics.1.1.out',args=>'--merge none');
+run_test(\&test_vcf_merge,$opts,in=>['merge.multiallelics.1.a','merge.multiallelics.1.b'],out=>'merge.multiallelics.1.1.out',args=>'--merge both');
 run_test(\&test_vcf_merge,$opts,in=>['merge.12.a','merge.12.b'],out=>'merge.12.1.out',args=>'--merge none');
 run_test(\&test_vcf_merge,$opts,in=>['merge.12.a','merge.12.b'],out=>'merge.12.1.out',args=>'--merge both');
 run_test(\&test_vcf_merge,$opts,in=>['merge.phased.1.a','merge.phased.1.b'],out=>'merge.phased.1.1.out',args=>'');
diff --git a/vcfmerge.c b/vcfmerge.c
@@ -3137,14 +3137,23 @@ int can_merge(args_t *args)
                 if ( strcmp(id,line->d.id) ) continue;      // matching by ID and it does not match the selected record
             }
             else if ( selected_types && !types_compatible(args,selected_types,buf,j) ) continue;
-            else
-            {
-                // First time here, choosing the first line: prioritize SNPs when available in the -m snps,both modes
-                if ( (args->collapse&COLLAPSE_SNPS || args->collapse==COLLAPSE_NONE)     // asked to merge SNVs into multiallelics
-                        && (maux->var_types&snp_mask)                   // there are SNVs at the current position
-                        && !(buf->rec[j].var_types&(snp_mask|ref_mask)) // and this record is not a SNV nor ref
-                   ) continue;
-            }
+
+            // This is not a good code. It makes the incorrect assumption of always having a SNP record available.
+            // However, that is not always the case and prevents the merging of G>GT,T with G>GT (see test/merge.multiallelics.1.*.vcf).
+            // We'd need to first check if it is possible to merge with something at all, and only then start excluding.
+            // Anyway, the can_merge() function should be about a *possibility*, one might argue that the priority should be handled in
+            // the stage_line() function.
+            // Commenting this out makes only one difference in our test case: reorders the output lines so that indels can come first.
+            //
+            //  else
+            //  {
+            //      // First time here, choosing the first line: prioritize SNPs when available in the -m snps,both modes
+            //      if ( (args->collapse&COLLAPSE_SNPS || args->collapse==COLLAPSE_NONE)     // asked to merge SNVs into multiallelics
+            //              && (maux->var_types&snp_mask)                   // there are SNVs at the current position
+            //              && !(buf->rec[j].var_types&(snp_mask|ref_mask)) // and this record is not a SNV nor ref
+            //         ) continue;
+            //  }
+
             selected_types |= line_types;
 
             buf->rec[j].skip = 0;   // the j-th record from i-th reader can be included. Final decision will be made in stage_line
