FILTER!=PASS but FT=PASS

[biozzq]

Dear @hannespetur

I found many variants are with "PASS" for FT but not FILTER, as the following example. Should I filter out these？Thanks for your attention.

1       273082885       1:273082885:FG  N       <INS:SVSIZE=131:AGGREGATED>     255     LowPratio       ABHet=-1;ABHetMulti=-1,-1;ABHom=1;ABHomMulti=-1,1;AC=2;AF=1;AN=2;CR=0;CRal=0,0;CRalt=0;END=273082885;MMal=0,149;MMalt=0.827778;MQ=68;MQSal=0,64800;MQalt=60;MQsquared=82800;MaxAAS=18;MaxAASR=1;MaxAltPP=18;NHet=0;NHomAlt=1;NHomRef=0;PASS_AC=0;PASS_AN=0;PASS_ratio=0;QD=25;QDalt=25;RELATED_SV_ID=5;RefLen=1;SB=0.5556;SBAlt=0.5556;SBF=0,10;SBF1=0,0;SBF2=0,10;SBR=0,8;SBR1=0,1;SBR2=0,7;SDal=0,1441;SDalt=80.0556;SEQ=TCTGTAGGGCCTGAGGCCGGCGCGGGGATCTGTGCAAAGCTTGTCAGGGAAGGGATTACACGGCCAGGGAATAGCCTTCCGTGTAATTCGGTGCCCGCCTGGTAAATGCCGAGCTTCCCTTTCCTGCCCCG;SVLEN=131;SVMODEL=AGGREGATED;SVSIZE=131;SVTYPE=INS;SV_ID=4;SeqDepth=18;VarType=FG        GT:FT:AD:MD:DP:RA:PP:GQ:PL      1/1:PASS:0,18:0:18:0,18:18:54:255,54,0
1       273082885       1:273082885:FG.0        N       <INS:SVSIZE=131:BREAKPOINT1>    255     PASS    ABHet=-1;ABHetMulti=-1,-1;ABHom=1;ABHomMulti=-1,1;AC=2;AF=1;AN=2;CR=0;CRal=0,0;CRalt=0;END=273082885;MMal=0,149;MMalt=0.827778;MQ=68;MQSal=0,64800;MQalt=60;MQsquared=82800;MaxAAS=18;MaxAASR=1;MaxAltPP=18;NHet=0;NHomAlt=1;NHomRef=0;PASS_AC=2;PASS_AN=2;PASS_ratio=1;QD=25;QDalt=25;RELATED_SV_ID=5;RefLen=1;SB=0.5556;SBAlt=0.5556;SBF=0,10;SBF1=0,0;SBF2=0,10;SBR=0,8;SBR1=0,1;SBR2=0,7;SDal=0,1441;SDalt=80.0556;SEQ=TCTGTAGGGCCTGAGGCCGGCGCGGGGATCTGTGCAAAGCTTGTCAGGGAAGGGATTACACGGCCAGGGAATAGCCTTCCGTGTAATTCGGTGCCCGCCTGGTAAATGCCGAGCTTCCCTTTCCTGCCCCG;SVLEN=131;SVMODEL=BREAKPOINT1;SVSIZE=131;SVTYPE=INS;SV_ID=4;SeqDepth=18;VarType=FG       GT:FT:AD:MD:DP:RA:PP:GQ:PL      1/1:PASS:0,18:0:18:0,18:18:54:255,54,0
1       273082885       1:273082885:FG.1        N       <INS:SVSIZE=131:BREAKPOINT2>    120     LowPratio       ABHet=-1;ABHetMulti=-1,-1;ABHom=1;ABHomMulti=-1,1;AC=2;AF=1;AN=2;CR=0;CRal=0,0;CRalt=0;END=273082885;MMal=0,13;MMalt=0.26;MQ=129;MQSal=0,18000;MQalt=60;MQsquared=82800;MaxAAS=5;MaxAASR=1;MaxAltPP=5;NHet=0;NHomAlt=1;NHomRef=0;PASS_AC=0;PASS_AN=0;PASS_ratio=0;QD=24;QDalt=24;RELATED_SV_ID=4;RefLen=1;SB=0.6;SBAlt=0.6;SBF=0,3;SBF1=0,1;SBF2=0,2;SBR=0,2;SBR1=0,0;SBR2=0,2;SDal=0,223;SDalt=44.6;SEQ=TCTGTAGGGCCTGAGGCCGGCGCGGGGATCTGTGCAAAGCTTGTCAGGGAAGGGATTACACGGCCAGGGAATAGCCTTCCGTGTAATTCGGTGCCCGCCTGGTAAATGCCGAGCTTCCCTTTCCTGCCCCG;SVLEN=131;SVMODEL=BREAKPOINT2;SVSIZE=131;SVTYPE=INS;SV_ID=5;SeqDepth=5;VarType=FG  GT:FT:AD:MD:DP:RA:PP:GQ:PL      1/1:FAIL2:0,5:0:5:0,5:5:15:120,15,0

Best wishes, Zheng zhuqing