8000 BND reference base disagreement · Issue #69 · friend1ws/nanomonsv · GitHub
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BND reference base disagreement #69

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readmanchiu opened this issue Dec 4, 2024 · 0 comments
Open

BND reference base disagreement #69

readmanchiu opened this issue Dec 4, 2024 · 0 comments

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@readmanchiu
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Hello,

Thanks for developing this useful tool. I am running v0.7.2. I found out that in the VCF output for some BND records the reference base reported in ALT does not agree with the base reported in REF. I posted some of the cases here. A simple example is the second record (chr19) where the REF column is an T but the base in the BND notation is an A. There are cases for which multiple bases are reported in the BND notation, which indicates an insertion sequence detected at the breakpoint. However, if I am not mistaken, the outermost base of the sequence at the BND should be the reference base and matches the base in REF. As you see in record 5 (chr5), none of the 2 bases in the BND notation ("CA") matches the T reported in REF. Are these potential errors?

chr1	54561076	r_1_0	T	]chr22:19448434]TTTTTTTC	.	PASS	SVTYPE=BND;MATEID=r_1_1;SVINSLEN=7;SVINSSEQ=TTTTTTT	TR:VR	69:5	57:1
chr19	44546299	r_107_0	T	[chr5:57983690[A	.	Too_low_VAF	SVTYPE=BND;MATEID=r_107_1	TR:VR	97:4	35:0
chr2	11789789	r_112_0	T	[chrX:42905347[TTTTTTTTTTTTTTTTTTTTTTTTTTTTTA	.	Too_low_VAF	SVTYPE=BND;MATEID=r_112_1;SVINSLEN=29;SVINSSEQ=TTTTTTTTTTTTTTTTTTTTTTTTTTTTT	TR:VR	89:4	55:1
chr3	151430756	r_156_0	C	[chr5:39787649[G	.	Too_low_VAF	SVTYPE=BND;MATEID=r_156_1	TR:VR	121:6	100:0
chr5	142000089	r_195_0	T	[chr9:33455109[CA	.	Too_low_VAF	SVTYPE=BND;MATEID=r_195_1;SVINSLEN=1;SVINSSEQ=C	TR:VR	76:3	46:1
chr1	83604376	r_3_0	T	]chr12:87749629]A	.	PASS	SVTYPE=BND;MATEID=r_3_1	TR:VR	103:6	66:0
chr17	72236544	r_99_0	A	[chr3:17063225[GC	.	Too_low_VAF	SVTYPE=BND;MATEID=r_99_1;SVINSLEN=1;SVINSSEQ=G	TR:VR	159:4	135:0
chr2	95927234	r_117_0	T	]chrX:125928884]A	.	Too_low_VAF	SVTYPE=BND;MATEID=r_117_1	TR:VR	207:5	83:0
chr22	12189934	r_140_0	G	]chr4:49324067]GCAGTTTCACTGAGTTACTCCCCTGTCTCTCTCATGTCTTCACCCCCAGCCCCCTGGGACTCTCCTGTCTGTCCCAGCTACTCCCCCACCACGCCCAGATTTCAGAGGGAA	.	Too_low_VAF	SVTYPE=BND;MATEID=r_140_1;SVINSLEN=110;SVINSSEQ=GCAGTTTCACTGAGTTACTCCCCTGTCTCTCTCATGTCTTCACCCCCAGCCCCCTGGGACTCTCCTGTCTGTCCCAGCTACTCCCCCACCACGCCCAGATTTCAGAGGGA	TR:VR	750:3	579:0
chr6	142128964	r_214_0	G	]chr7:25047879]CT	.	PASS	SVTYPE=BND;MATEID=r_214_1;SVINSLEN=1;SVINSSEQ=C	TR:VR	125:11	85:1
chr1	105290676	r_7_0	A	[chrUn_KI270590v1:3[T	.	Too_low_VAF	SVTYPE=BND;MATEID=r_7_1	TR:VR	155:3	101:0
chr11	10020893	r_31_0	C	]chr3:159101396]A	.	PASS	SVTYPE=BND;MATEID=r_31_1	TR:VR	93:14	46:0
chr15	58263222	r_66_0	T	[chr15:58263227[C	.	PASS	SVTYPE=BND;MATEID=r_66_1	TR:VR	44:3	20:0
chr16	34062745	r_73_0	C	[chrY:56843856[TGTGTCACAATGCCCATGTAGGCAGAGCCTAGGCAAGAGCTACAACATCTGAGTGATCAATGCAGTGATATGTCACTATGCCCCAATAGGCAGAGCATAGTCAAGTGTTACATCACTTGGGTGATCAGTGCAGAGATAGGTCACAATGCCCACATACACAGAGACTATAAAATATTCTCATCACT	.	Too_low_VAF	SVTYPE=BND;MATEID=r_73_1;SVINSLEN=184;SVINSSEQ=TGTGTCACAATGCCCATGTAGGCAGAGCCTAGGCAAGAGCTACAACATCTGAGTGATCAATGCAGTGATATGTCACTATGCCCCAATAGGCAGAGCATAGTCAAGTGTTACATCACTTGGGTGATCAGTGCAGAGATAGGTCACAATGCCCACATACACAGAGACTATAAAATATTCTCATCAC	TR:VR905:5	638:1
fail:chrUn_KI270746v1	28446	r_234_0	A	[chrUn_KI270746v1:34429[C	.	Too_low_VAF	SVTYPE=BND;MATEID=r_234_1	TR:VR	299:4	81:1
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