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20 hours ago •
DecodeGenetics
DecodeGenetics
FILTER!=PASS but FT=PASS
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
I have a similar issue: FILTER="LowPratio", PASS_AC=0, but many samples have FT of "PASS"
10616 1:10616:DG N <DEL:SVSIZE=137:AGGREGATED>
20124 LowPratio ABHet=-1;ABHetMulti=-1,-1;ABHom=0.9903;ABHomMulti=-1,0.9903;AC=160;AF=1;AN=160;CR=0;CRal=0,0;CRalt=0;END=10753;MMal=0,99;MMalt=0.0034555;MQ=4;MQSal=0,50860;MQalt=4;MQsquared=50860;MaxAAS=70;MaxAASR=1;MaxAltPP=0;NHet=0;NHomAlt=80;NHomRef=0;NUM_MERGED_SVS=1;PASS_AC=0;PASS_AN=0;PASS_ratio=0;QD=24.71;QDalt=24.71;RefLen=1;SB=0.2353;SBAlt=0.2353;SBF=0,4;SBF1=0,4;SBF2=0,0;SBR=0,13;SBR1=0,11;SBR2=0,2;SDal=0,407;SDalt=0.142059;SVLEN=137;SVMODEL=AGGREGATED;SVSIZE=137;SVTYPE=DEL;SV_ID=1;SeqDepth=2893;VarType=DG GT:FT:AD:MD:DP:RA:PP:GQ:PL 1/1:PASS:0,30:0:30:0,0:0:90:255,90,0
1/1:PASS:0,42:0:42:0,0:0:99:255,126,0 1/1:PASS:0,34:0:34:0,0:0:99:255,102,0 1/1:PASS:0,43:0:43:0,0:0:99:255,129,0 1/1:PASS:0,39:0:39:0,0:0:99:255,117,0 1/1:PASS:0,35:0:35:0,0:0:99:255,105,0 1/1:PASS:0,31:0:31:0,0:0:93:255,93,0 1/1:PASS:1,46:0:47:0,0:0:99:255,129,0 1/1:PASS:0,43:0:43:0,0:0:99:255,129,0 1/1:PASS:0,42:0:42:0,0:0:99:255,126,0 1/1:PASS:0,36:0:36:0,0:0:99:255,108,0 1/1:PASS:0,40:0:40:0,0:0:99:255,120,0 1/1:PASS:0,38:0:38:0,0:0:99:255,114,0 1/1:PASS:0,38:0:38:0,0:0:99:255,114,0 1/1:PASS:0,31:0:31:0,0:0:93:255,93,0 1/1:PASS:0,41:0:41:0,0:0:99:255,123,0 1/1:PASS:0,43:0:43:0,0:0:99:255,129,0 1/1:PASS:0,27:0:27:0,0:0:81:255,81,0 1/1:PASS:0,31:0:31:0,0:0:93:255,93,0
