How is variant type determined?

[shaze]

How does Truvari determine variant type?

From the ALT field? Or from an SVTYPE or SIMPLE_TYPE annotation?

Thanks

Scott

[ACEnglish]

See developer documentation here

Starts by trying to use INFO/SVTYPE

If SVTYPE is unavailable, infer if entry is a insertion or deletion by looking at the REF/ALT sequence size differences

If REF/ALT sequences are not available, try to parse the <INS>, <DEL>, etc from the ALT column.

Otherwise, assume ‘UNK’

[shaze]

Thanks -- that's helpful

FYI, gridss produces calls like this:

chr1    16192799        gridss1fb_4425h T       ]chr1:16192798]TATATATATATATATATATATATAT        1011.28 PASS    ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=3;ASC=1X;ASQ=626.25;ASRP=3;ASSR=29;BA=0;BAQ=0;BASRP=0;BASSR=0;BEID=asm1-13942,asm1-13962,asm1-36713,asm1-36716,asm1-36719;BEIDH=20,3,0,20,0;BEIDL=20,3,0,20,0;BMQ=60;BMQN=60;BMQX=60;BQ=195.17;BSC=5;BSCQ=100.82;BUM=4;BUMQ=94.35;BVF=1;CAS=0;CASQ=0;CQ=1011.28;EVENT=gridss1fb_4425;IC=5;IHOMPOS=0,0;IQ=135.84;MATEID=gridss1fb_4425o;MQ=53.8;MQN=25;MQX=60;RAS=2;RASQ=249.19;REF=17;REFPAIR=10;RP=0;RPQ=0;SB=0.55102;SC=1X80M;SR=0;SRQ=0;SVTYPE=BND;SVLEN=24;VF=19;SIMPLE_TYPE=INS       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        .:0.528:0:0:0:0:626.25:3:29:0:0:0:195.17:5:100.82:4:94.35:1:0:5:135.84:1011.28:249.19:17:10:0:0:0:0:19

I have written a script for my own purposes that uses SIMPLE_TYPE so now that I know I am OK, but just so you can see why I asked.