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22 months ago
qqq2395
•
0
Can anyone please point me out to the description of the relationship between the ID names in SV VCF file (mine is from svaba) What does the VCF include both one ends with :1 and the one with :2. Isn't that the same event? 2271991796:1 2271991796:2 Thank you
tpg|BK006946.2| 924303 2271991796:1 A ]tpg|BK006946.2|:924542]A 12 PASS DISC_MAPQ=20;EVDNC=DSCRD;IMPRECISE;MAPQ=20;MATEID=2271991796:2;MATENM=-1;NM=-1;NUMPARTS=0;SCTG=tpg|BK006946.2|:924303(-)-tpg|BK006946.2|:924542(+)__15_906501_924431D;SPAN=239;SVTYPE=BND GT:AD:DP:GQ:PL:SR:DR:LR:LO 0/1:9:62:12.5:12.5,0,141.2:0:9:-12.28:18.85
tpg|BK006946.2| 924542 2271991796:2 G G[tpg|BK006946.2|:924303[ 12 PASS DISC_MAPQ=18;EVDNC=DSCRD;IMPRECISE;MAPQ=18;MATEID=2271991796:1;MATENM=-1;NM=-1;NUMPARTS=0;SCTG=tpg|BK006946.2|:924303(-)-tpg|BK006946.2|:924542(+)__15_906501_924431D;SPAN=239;SVTYPE=BND GT:AD:DP:GQ:PL:SR:DR:LR:LO 0/1:9:62:12.5:12.5,0,141.2:0:9:-12.28:18.85
It's a BND (breakends) event. There are several SV types that can be included in BND, like translocation, inversion, and so on. I think the records you provided are only a part of this BND event, which means the two lines above should be together with other lines to tell a story. I would say it looks like a reversion with not 100% sure. Would you like to paste other BND records surrounding the two records?
To understand BND, this video is a good start, then you can read The Variant Call Format (VCF) Version 4.2 Specification to dig deeper. Hopefully, be helpful.