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Reciprocal transclocations #691

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cv55 opened this issue Feb 8, 2025 · 0 comments
Open

Reciprocal transclocations #691

cv55 opened this issue Feb 8, 2025 · 0 comments

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@cv55
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cv55 commented Feb 8, 2025

Hello, thanks for the great tool.

After running Gridss and Gripss for filtering I end up with ~20 BND events in my Vcf file. I noticed that every event has two lines in the Vcf file corresponding to the breakends at the two invlolved chromosomes. Here is an example:
chr1 73133711 gridss7ff_3636o T T]chr11:98061548] 742.31 PASS ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=1;ASC=243M1X;ASQ=246.19;ASRP=12;ASSR=13;BA=0;BAQ=0;BASRP=0;BASSR=0;BEID=asm190-70408,asm7-24298;BEIDH=0,244;BEIDL=287,0;BMQ=60;BMQN=60;BMQX=60;BQ=18.99;BSC=1;BSCQ=18.99;BUM=0;BUMQ=0;BVF=0;CAS=0;CASQ=0;CQ=742.31;EVENT=gridss7ff_3636;IC=0;IHOMPOS=0,0;IQ=0;MATEID=gridss7ff_3636h;MQ=59.15;MQN=39;MQX=60;RAS=1;RASQ=268.91;REF=206;REFPAIR=34;RP=6;RPQ=107.97;SB=0.5263158;SC=243M1X;SR=5;SRQ=119.23;SVTYPE=BND;TAF=0.06;VF=8 GT:AF:ANRP:ANRPQ:ANSR:ANSRQ:ASQ:ASRP:ASSR:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:101:14:0:0:0:0:0 .:0.06:0:0:0:0:246.19:12:13:0:0:0:18.99:1:18.99:0:0:0:0:0:0:742.31:268.91:105:20:6:107.97:5:119.23:8
chr11 98061548 gridss7ff_3636h G G]chr1:73133711] 742.31 PASS ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=1;ASC=285M1X;ASQ=268.91;ASRP=12;ASSR=13;BA=0;BAQ=0;BASRP=0;BASSR=0;BEID=asm190-70408,asm7-24298;BEIDH=287,0;BEIDL=0,244;BMQ=60;BMQN=60;BMQX=60;BQ=74.3;BSC=2;BSCQ=41.71;BUM=1;BUMQ=32.58;BVF=1;CAS=0;CASQ=0;CQ=742.31;EVENT=gridss7ff_3636;IC=0;IHOMPOS=0,0;IQ=0;MATEID=gridss7ff_3636o;MQ=59.15;MQN=39;MQX=60;RAS=1;RASQ=246.19;REF=185;REFPAIR=33;RP=6;RPQ=107.97;SB=0.55;SC=285M1X;SR=5;SRQ=119.23;SVTYPE=BND;TAF=0.072;VF=8 GT:AF:ANRP:ANRPQ:ANSR:ANSRQ:ASQ:ASRP:ASSR:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0:0:0:0:0:0:0:0:0:0:0:32.58:0:0:1:32.58:1:0:0:0:0:0:99:16:0:0:0:0:0 .:0.072:0:0:0:0:268.91:12:13:0:0:0:41.71:2:41.71:0:0:0:0:0:0:742.31:246.19:86:17:6:107.97:5:119.23:8

Is it safe to assume that all these BND events are reciprocal?

Thanks a lot.

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