VCF SV basic question: ids a:1 & a:2
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7 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
vcf SVs svaba • 224 views
Entering edit mode

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.


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