Stochastic behaviour of GRIDSS

[gseryogin]

Hi!

GRIDSS clearly has non-deterministic behaviour:

1. it produces different number of rows in vcf file ater each rerun on the same set of bam files (which means variant can be accidentially lost after rerun)
2. it may assign different values to QUAL or VF for the same variant after rerun

Here is my example: I ran 6 times completely the same job (8cpu and 32gb) with gridss for the same set of bam files (1 normal samples + 2 tumor samples) and each time got different results for the event of interest:

chr10   32016769        gridss170bb_33o C       [chr10:43111683[C       514.58  SINGLE_ASSEMBLY ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=0;ASC=2X107M;ASQ=0;ASRP=0;ASSR=21;BA=0;BAQ=0;BASRP=0;BASSR=0;BEID=asm172-3974;BEIDH=108;BEIDL=0;BQ=0;BSC=0;BSCQ=0;BUM=0;BUMQ=0;BVF=0;CAS=0;CASQ=0;CIPOS=0,1;CIRPOS=-1,0;CQ=514.58;EVENT=gridss170bb_33;HOMLEN=1;HOMSEQ=C;IC=0;IHOMPOS=0,1;IQ=0;MATEID=gridss170bb_33h;MQ=60;MQN=60;MQX=60;RAS=1;RASQ=465.22;REF=26;REFPAIR=0;RP=0;RPQ=0;SB=0.521739;SC=2X107M;SR=2;SRQ=49.37;SVTYPE=BND;VF=15;SIMPLE_SVTYPE=INV;SIMPLE_SVLEN=11094913  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        .:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:3:0:0:0:0:0:0 .:0.333:0:0:0:0:0:0:9:0:0:0:0:0:0:0:0:0:0:0:0:256.41:207.04:12:0:0:0:2:49.37:6  .:0.45:0:0:0:0:0:0:12:0:0:0:0:0:0:0:0:0:0:0:0:258.17:258.17:11:0:0:0:0:0:9
chr10   43111683        gridss170bb_33h C       [chr10:32016769[C       514.58  SINGLE_ASSEMBLY ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=1;ASC=2X;ASQ=465.22;ASRP=0;ASSR=21;BA=0;BAQ=0;BASRP=0;BASSR=0;BEID=asm172-3974;BEIDH=0;BEIDL=108;BMQ=60;BMQN=60;BMQX=60;BQ=771.15;BSC=27;BSCQ=591.15;BUM=3;BUMQ=180;BVF=4;CAS=0;CASQ=0;CIPOS=-1,0;CIRPOS=0,1;CQ=514.58;EVENT=gridss170bb_33;HOMLEN=1;HOMSEQ=G;IC=0;IHOMPOS=-1,0;IQ=0;MATEID=gridss170bb_33o;MQ=60;MQN=60;MQX=60;RAS=0;RASQ=0;REF=10249;REFPAIR=0;RP=0;RPQ=0;SB=0.54;SC=2X60M;SR=2;SRQ=49.37;SVTYPE=BND;VF=15;SIMPLE_SVTYPE=INV;SIMPLE_SVLEN=11094913   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        .:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:3328:0:0:0:0:0:0      .:0.001799:0:0:0:0:207.04:0:9:0:0:0:241.32:8:181.32:1:60:1:0:0:0:256.41:0:3329:0:0:0:2:49.37:6      .:0.002499:0:0:0:0:258.17:0:12:0:0:0:529.83:19:409.83:2:120:3:0:0:0:258.17:0:3592:0:0:0:0:0:9

chr10   32016769        gridss170bb_33o C       [chr10:43111683[C       484.62  LOW_QUAL;SINGLE_ASSEMBLY        ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=0;ASC=2X107M;ASQ=0;ASRP=0;ASSR=20;BA=0;BAQ=0;BASRP=0;BASSR=0;BEID=asm172-4013;BEIDH=108;BEIDL=0;BQ=0;BSC=0;BSCQ=0;BUM=0;BUMQ=0;BVF=0;CAS=0;CASQ=0;CIPOS=0,1;CIRPOS=-1,0;CQ=484.62;EVENT=gridss170bb_33;HOMLEN=1;HOMSEQ=C;IC=0;IHOMPOS=0,1;IQ=0;MATEID=gridss170bb_33h;MQ=60;MQN=60;MQX=60;RAS=1;RASQ=435.26;REF=26;REFPAIR=0;RP=0;RPQ=0;SB=0.454545;SC=2X107M;SR=2;SRQ=49.37;SVTYPE=BND;VF=16;SIMPLE_SVTYPE=INV;SIMPLE_SVLEN=11094913  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        .:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:3:0:0:0:0:0:0     .:0.333:0:0:0:0:0:0:7:0:0:0:0:0:0:0:0:0:0:0:0:208:158.64:12:0:0:0:2:49.37:6 .:0.476:0:0:0:0:0:0:13:0:0:0:0:0:0:0:0:0:0:0:0:276.62:276.62:11:0:0:0:0:0:10
chr10   43111683        gridss170bb_33h C       [chr10:32016769[C       484.62  LOW_QUAL;SINGLE_ASSEMBLY        ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=1;ASC=2X;ASQ=435.26;ASRP=0;ASSR=20;BA=0;BAQ=0;BASRP=0;BASSR=0;BEID=asm172-4013;BEIDH=0;BEIDL=108;BMQ=60;BMQN=60;BMQX=60;BQ=771.15;BSC=27;BSCQ=591.15;BUM=3;BUMQ=180;BVF=3;CAS=0;CASQ=0;CIPOS=-1,0;CIRPOS=0,1;CQ=484.62;EVENT=gridss170bb_33;HOMLEN=1;HOMSEQ=G;IC=0;IHOMPOS=-1,0;IQ=0;MATEID=gridss170bb_33o;MQ=60;MQN=60;MQX=60;RAS=0;RASQ=0;REF=10249;REFPAIR=0;RP=0;RPQ=0;SB=0.510204;SC=2X60M;SR=2;SRQ=49.37;SVTYPE=BND;VF=16;SIMPLE_SVTYPE=INV;SIMPLE_SVLEN=11094913       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        .:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:3328:0:0:0:0:0:0  .:0.001799:0:0:0:0:158.64:0:7:0:0:0:241.32:8:181.32:1:60:1:0:0:0:208:0:3329:0:0:0:2:49.37:6 .:0.002776:0:0:0:0:276.62:0:13:0:0:0:529.83:19:409.83:2:120:2:0:0:0:276.62:0:3592:0:0:0:0:0:10

chr10   32016769        gridss170bb_33o C       [chr10:43111683[C       563.27  SINGLE_ASSEMBLY ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=0;ASC=2X107M;ASQ=0;ASRP=0;ASSR=23;BA=0;BAQ=0;BASRP=0;BASSR=0;BEID=asm172-3644;BEIDH=108;BEIDL=0;BQ=0;BSC=0;BSCQ=0;BUM=0;BUMQ=0;BVF=0;CAS=0;CASQ=0;CIPOS=0,1;CIRPOS=-1,0;CQ=563.27;EVENT=gridss170bb_33;HOMLEN=1;HOMSEQ=C;IC=0;IHOMPOS=0,1;IQ=0;MATEID=gridss170bb_33h;MQ=60;MQN=60;MQX=60;RAS=1;RASQ=513.9;REF=26;REFPAIR=0;RP=0;RPQ=0;SB=0.6;SC=2X107M;SR=2;SRQ=49.37;SVTYPE=BND;VF=15;SIMPLE_SVTYPE=INV;SIMPLE_SVLEN=11094913        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        .:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:3:0:0:0:0:0:0     .:0.333:0:0:0:0:0:0:9:0:0:0:0:0:0:0:0:0:0:0:0:257.39:208.03:12:0:0:0:2:49.37:6      .:0.45:0:0:0:0:0:0:14:0:0:0:0:0:0:0:0:0:0:0:0:305.88:305.88:11:0:0:0:0:0:9
chr10   43111683        gridss170bb_33h C       [chr10:32016769[C       563.27  SINGLE_ASSEMBLY ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=1;ASC=2X;ASQ=513.9;ASRP=0;ASSR=23;BA=0;BAQ=0;BASRP=0;BASSR=0;BEID=asm172-3644;BEIDH=0;BEIDL=108;BMQ=60;BMQN=60;BMQX=60;BQ=771.15;BSC=27;BSCQ=591.15;BUM=3;BUMQ=180;BVF=4;CAS=0;CASQ=0;CIPOS=-1,0;CIRPOS=0,1;CQ=563.27;EVENT=gridss170bb_33;HOMLEN=1;HOMSEQ=G;IC=0;IHOMPOS=-1,0;IQ=0;MATEID=gridss170bb_33o;MQ=60;MQN=60;MQX=60;RAS=0;RASQ=0;REF=10249;REFPAIR=0;RP=0;RPQ=0;SB=0.576923;SC=2X60M;SR=2;SRQ=49.37;SVTYPE=BND;VF=15;SIMPLE_SVTYPE=INV;SIMPLE_SVLEN=11094913        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        .:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:3328:0:0:0:0:0:0  .:0.001799:0:0:0:0:208.03:0:9:0:0:0:241.32:8:181.32:1:60:1:0:0:0:257.39:0:3329:0:0:0:2:49.37:6      .:0.002499:0:0:0:0:305.88:0:14:0:0:0:529.83:19:409.83:2:120:3:0:0:0:305.88:0:3592:0:0:0:0:0:9

chr10   32016769        gridss170bb_33o C       [chr10:43111683[C       453.65  LOW_QUAL;SINGLE_ASSEMBLY        ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=0;ASC=2X107M;ASQ=0;ASRP=0;ASSR=18;BA=0;BAQ=0;BASRP=0;BASSR=0;BEID=asm172-3776;BEIDH=108;BEIDL=0;BQ=0;BSC=0;BSCQ=0;BUM=0;BUMQ=0;BVF=0;CAS=0;CASQ=0;CIPOS=0,1;CIRPOS=-1,0;CQ=453.65;EVENT=gridss170bb_33;HOMLEN=1;HOMSEQ=C;IC=0;IHOMPOS=0,1;IQ=0;MATEID=gridss170bb_33h;MQ=60;MQN=60;MQX=60;RAS=1;RASQ=404.28;REF=26;REFPAIR=0;RP=0;RPQ=0;SB=0.5;SC=2X107M;SR=2;SRQ=49.37;SVTYPE=BND;VF=12;SIMPLE_SVTYPE=INV;SIMPLE_SVLEN=11094913       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        .:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:3:0:0:0:0:0:0     .:0.25:0:0:0:0:0:0:7:0:0:0:0:0:0:0:0:0:0:0:0:213.64:164.27:12:0:0:0:2:49.37:4       .:0.421:0:0:0:0:0:0:11:0:0:0:0:0:0:0:0:0:0:0:0:240.01:240.01:11:0:0:0:0:0:8
chr10   43111683        gridss170bb_33h C       [chr10:32016769[C       453.65  LOW_QUAL;SINGLE_ASSEMBLY        ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=1;ASC=2X;ASQ=404.28;ASRP=0;ASSR=18;BA=0;BAQ=0;BASRP=0;BASSR=0;BEID=asm172-3776;BEIDH=0;BEIDL=108;BMQ=60;BMQN=60;BMQX=60;BQ=771.15;BSC=27;BSCQ=591.15;BUM=3;BUMQ=180;BVF=7;CAS=0;CASQ=0;CIPOS=-1,0;CIRPOS=0,1;CQ=453.65;EVENT=gridss170bb_33;HOMLEN=1;HOMSEQ=G;IC=0;IHOMPOS=-1,0;IQ=0;MATEID=gridss170bb_33o;MQ=60;MQN=60;MQX=60;RAS=0;RASQ=0;REF=10249;REFPAIR=0;RP=0;RPQ=0;SB=0.531915;SC=2X60M;SR=2;SRQ=49.37;SVTYPE=BND;VF=12;SIMPLE_SVTYPE=INV;SIMPLE_SVLEN=11094913       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        .:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:3328:0:0:0:0:0:0  .:0.0012:0:0:0:0:164.27:0:7:0:0:0:241.32:8:181.32:1:60:3:0:0:0:213.64:0:3329:0:0:0:2:49.37:4        .:0.002222:0:0:0:0:240.01:0:11:0:0:0:529.83:19:409.83:2:120:4:0:0:0:240.01:0:3592:0:0:0:0:0:8

chr10   32016769        gridss170bb_33o C       [chr10:43111683[C       491.22  LOW_QUAL;SINGLE_ASSEMBLY        ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=0;ASC=2X107M;ASQ=0;ASRP=0;ASSR=20;BA=0;BAQ=0;BASRP=0;BASSR=0;BEID=asm172-4005;BEIDH=108;BEIDL=0;BQ=0;BSC=0;BSCQ=0;BUM=0;BUMQ=0;BVF=0;CAS=0;CASQ=0;CIPOS=0,1;CIRPOS=-1,0;CQ=491.22;EVENT=gridss170bb_33;HOMLEN=1;HOMSEQ=C;IC=0;IHOMPOS=0,1;IQ=0;MATEID=gridss170bb_33h;MQ=60;MQN=60;MQX=60;RAS=1;RASQ=441.85;REF=26;REFPAIR=0;RP=0;RPQ=0;SB=0.545455;SC=2X107M;SR=2;SRQ=49.37;SVTYPE=BND;VF=15;SIMPLE_SVTYPE=INV;SIMPLE_SVLEN=11094913  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        .:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:3:0:0:0:0:0:0     .:0.333:0:0:0:0:0:0:9:0:0:0:0:0:0:0:0:0:0:0:0:254.34:204.97:12:0:0:0:2:49.37:6      .:0.45:0:0:0:0:0:0:11:0:0:0:0:0:0:0:0:0:0:0:0:236.88:236.88:11:0:0:0:0:0:9
chr10   43111683        gridss170bb_33h C       [chr10:32016769[C       491.22  LOW_QUAL;SINGLE_ASSEMBLY        ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=1;ASC=2X;ASQ=441.85;ASRP=0;ASSR=20;BA=0;BAQ=0;BASRP=0;BASSR=0;BEID=asm172-4005;BEIDH=0;BEIDL=108;BMQ=60;BMQN=60;BMQX=60;BQ=771.15;BSC=27;BSCQ=591.15;BUM=3;BUMQ=180;BVF=4;CAS=0;CASQ=0;CIPOS=-1,0;CIRPOS=0,1;CQ=491.22;EVENT=gridss170bb_33;HOMLEN=1;HOMSEQ=G;IC=0;IHOMPOS=-1,0;IQ=0;MATEID=gridss170bb_33o;MQ=60;MQN=60;MQX=60;RAS=0;RASQ=0;REF=10249;REFPAIR=0;RP=0;RPQ=0;SB=0.55102;SC=2X60M;SR=2;SRQ=49.37;SVTYPE=BND;VF=15;SIMPLE_SVTYPE=INV;SIMPLE_SVLEN=11094913        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        .:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:3328:0:0:0:0:0:0  .:0.001799:0:0:0:0:204.97:0:9:0:0:0:241.32:8:181.32:1:60:1:0:0:0:254.34:0:3329:0:0:0:2:49.37:6      .:0.002499:0:0:0:0:236.88:0:11:0:0:0:529.83:19:409.83:2:120:3:0:0:0:236.88:0:3592:0:0:0:0:0:9

chr10	32016769	gridss170bb_33o	C	[chr10:43111683[C	490.06	LOW_QUAL;SINGLE_ASSEMBLY	ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=0;ASC=2X107M;ASQ=0;ASRP=0;ASSR=20;BA=0;BAQ=0;BASRP=0;BASSR=0;BEID=asm172-3772;BEIDH=108;BEIDL=0;BQ=0;BSC=0;BSCQ=0;BUM=0;BUMQ=0;BVF=0;CAS=0;CASQ=0;CIPOS=0,1;CIRPOS=-1,0;CQ=490.06;EVENT=gridss170bb_33;HOMLEN=1;HOMSEQ=C;IC=0;IHOMPOS=0,1;IQ=0;MATEID=gridss170bb_33h;MQ=60;MQN=60;MQX=60;RAS=1;RASQ=440.69;REF=26;REFPAIR=0;RP=0;RPQ=0;SB=0.545455;SC=2X107M;SR=2;SRQ=49.37;SVTYPE=BND;VF=13;SIMPLE_SVTYPE=INV;SIMPLE_SVLEN=11094913	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	.:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:3:0:0:0:0:0:0	.:0.294:0:0:0:0:0:0:8:0:0:0:0:0:0:0:0:0:0:0:0:233.66:184.29:12:0:0:0:2:49.37:5	.:0.421:0:0:0:0:0:0:12:0:0:0:0:0:0:0:0:0:0:0:0:256.4:256.4:11:0:0:0:0:0:8
chr10	43111683	gridss170bb_33h	C	[chr10:32016769[C	490.06	LOW_QUAL;SINGLE_ASSEMBLY	ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=1;ASC=2X;ASQ=440.69;ASRP=0;ASSR=20;BA=0;BAQ=0;BASRP=0;BASSR=0;BEID=asm172-3772;BEIDH=0;BEIDL=108;BMQ=60;BMQN=60;BMQX=60;BQ=771.15;BSC=27;BSCQ=591.15;BUM=3;BUMQ=180;BVF=6;CAS=0;CASQ=0;CIPOS=-1,0;CIRPOS=0,1;CQ=490.06;EVENT=gridss170bb_33;HOMLEN=1;HOMSEQ=G;IC=0;IHOMPOS=-1,0;IQ=0;MATEID=gridss170bb_33o;MQ=60;MQN=60;MQX=60;RAS=0;RASQ=0;REF=10249;REFPAIR=0;RP=0;RPQ=0;SB=0.55102;SC=2X60M;SR=2;SRQ=49.37;SVTYPE=BND;VF=13;SIMPLE_SVTYPE=INV;SIMPLE_SVLEN=11094913	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	.:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:3328:0:0:0:0:0:0	.:0.0015:0:0:0:0:184.29:0:8:0:0:0:241.32:8:181.32:1:60:2:0:0:0:233.66:0:3329:0:0:0:2:49.37:5	.:0.002222:0:0:0:0:256.4:0:12:0:0:0:529.83:19:409.83:2:120:4:0:0:0:256.4:0:3592:0:0:0:0:0:8

What is more concserning, is that on the 7th time this paired breakpoint converted to sigle breakend:

chr10	43111682	gridss172b_309b	G	.CCTGTAATCCCAACACTTTGGGAGGTCGAGGCGGGTGGATCACCTG	1100.22	LOW_QUAL	ANRP=0;ANRPQ=0;ANSR=0;ANSRQ=0;AS=0;ASC=1X;ASQ=0;ASRP=0;ASSR=0;BA=1;BAQ=329.06;BASRP=0;BASSR=15;BEALN=chr7:6967118|+|45M|0;BEID=asm172-3936;BEIDH=-1;BEIDL=45;BMQ=60;BMQN=60;BMQX=60;BQ=1100.22;BSC=27;BSCQ=591.15;BUM=3;BUMQ=180;BVF=18;CAS=0;CASQ=0;CQ=1100.22;EVENT=gridss172b_309;IC=0;INSRM=AluSp#SINE/Alu|22|+|45M|389|3;INSRMP=1;INSRMRC=SINE/Alu;INSRMRO=+;INSRMRT=AluSp;IQ=0;RAS=0;RASQ=0;REF=10249;REFPAIR=0;RP=0;RPQ=0;SB=0.547619;SC=1X;SR=0;SRQ=0;SVTYPE=BND;VF=0;SIMPLE_SVTYPE=BND	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	.:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:3328:0:0:0:0:0:0	.:0.001799:0:0:0:0:0:0:0:91.04:0:4:332.37:8:181.32:1:60:6:0:0:0:0:0:3329:0:0:0:0:0:0	.:0.00333:0:0:0:0:0:0:0:238.02:0:11:767.85:19:409.83:2:120:12:0:0:0:0:0:3592:0:0:0:0:0:0

I presume, that is a side effect of parallelism on assembly step (since all these variants has different asm ids). Is there any way to fix it, providing any parameter like seed or anything similar?

[gseryogin]

Even running gridss with --threads 1 does not help, number of rows still differ and all the values fluctuate the same way...

[d-cameron]

Do *_metrics differ? -> input files are different between runs?
Do the input.bam.sv.bam file differ? -> introduced by the call to bwa mem for soft clip realignment
Do the assembly.bam files differ? -> introduced by the GRIDSS assembler
Do the assembly.bam.sv.bam files differ? -> introduced by the call to bwa mem for assembly realignment
Do the output.breakpoint.vcf files differ? -> introduced by max-clique candidate identification
Do the output.vcf files differ? -> introduced by final evidence allocation

[d-cameron]

May need to run with --keepTempFiles to check each stage.

[gseryogin]

Do *_metrics differ? -> No
Do the input.bam.sv.bam file differ? -> No
Do the assembly.bam files differ? -> Yes
Do the assembly.bam.sv.bam files differ? -> Yes
Do the output.breakpoint.vcf files differ? -> Yes
Do the output.vcf files differ? -> Yes

So it looks like everything starts to diverge right after the GRIDSS assembler step

[gseryogin]

@d-cameron Hi!
Could please help to debug the GRIDSS assembler and localize the irreproducible step within it?

[madelonst]

@d-cameron First of all, thanks on your efforts on making GRIDSS available as a resource. We are encountering the same issue as reported by @gseryogin unfortunately.

In our case also, the content of the assembly.bam is different between runs and the output starts to diverge from there, regardless of running single- or multi-threaded. The issue seems more prominent in regions with mapping difficulty (for example MUC family genes, homopolymer stretches, tandem-repeat regions) and for regions where we have polyG-artifacts present from Illumina sequencing. We are using GRIDSS v2.13.2 in the pre-built docker image. Happy to share further details of differences spotted where needed.

Appreciate your kind assistance on this matter,
Madelon