/dports/biology/vt/vt-0.57721/test/normalize/ |
H A D | 01_IN.vcf | 101 20 1728298 . G GT . PASS VC=INDEL;AC=199;AF=0.63;AN=316 102 20 2171402 . T TA . PASS VC=INDEL;AC=223;AF=0.71;AN=316 116 20 6362163 . GC G . PASS VC=INDEL;AC=49;AF=0.2;AN=250 130 20 12840733 . C CT . PASS VC=INDEL;AC=8;AF=0.03;AN=316 146 20 17187630 . C CT . PASS VC=INDEL;AC=0;AF=0;AN=316 213 20 39475162 . TG T . PASS VC=INDEL;AC=1;AF=0;AN=250 222 20 42493962 . T TA . PASS VC=INDEL;AC=0;AF=0;AN=316 248 20 51055421 . AC A . PASS VC=INDEL;AC=0;AF=0;AN=296 251 20 51512776 . TCT T . PASS VC=INDEL;AC=0;AF=0;AN=316 270 20 56564760 . C CT . PASS VC=INDEL;AC=0;AF=0;AN=312 [all …]
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H A D | 01_OUT.vcf | 102 20 1728298 . G GT . PASS VC=INDEL;AC=199;AF=0.63;AN=316 103 20 2171402 . T TA . PASS VC=INDEL;AC=223;AF=0.71;AN=316 113 20 5509358 . T TG . PASS VC=INDEL;AC=136;AF=0.43;AN=316 116 20 6351757 . C CTT . PASS VC=INDEL;AC=52;AF=0.17;AN=314 117 20 6362163 . GC G . PASS VC=INDEL;AC=49;AF=0.2;AN=250 131 20 12840733 . C CT . PASS VC=INDEL;AC=8;AF=0.03;AN=316 147 20 17187630 . C CT . PASS VC=INDEL;AC=0;AF=0;AN=316 214 20 39475162 . TG T . PASS VC=INDEL;AC=1;AF=0;AN=250 223 20 42493962 . T TA . PASS VC=INDEL;AC=0;AF=0;AN=316 249 20 51055421 . AC A . PASS VC=INDEL;AC=0;AF=0;AN=296 [all …]
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/dports/biology/py-crossmap/CrossMap-0.5.4/test/ |
H A D | test02_hg19.vcf | 130 …0.0037;AFR_AF=0.02;AN=2184;AVGPOST=0.9976;ERATE=0.0010;LDAF=0.0042;RSQ=0.7479;THETA=0.0149;VT=INDEL 140 …0.0027;AFR_AF=0.01;AN=2184;AVGPOST=0.9255;ERATE=0.0049;LDAF=0.0407;RSQ=0.1292;THETA=0.0230;VT=INDEL 172 …F=0.01;AFR_AF=0.02;AN=2184;AVGPOST=0.9950;ERATE=0.0008;LDAF=0.0073;RSQ=0.7270;THETA=0.0063;VT=INDEL 198 …F=0.01;AFR_AF=0.03;AN=2184;AVGPOST=0.9988;ERATE=0.0005;LDAF=0.0066;RSQ=0.9279;THETA=0.0085;VT=INDEL 219 …F=0.01;AFR_AF=0.04;AN=2184;AVGPOST=0.9945;ERATE=0.0013;LDAF=0.0108;RSQ=0.7876;THETA=0.0026;VT=INDEL 224 …F=0.01;AN=2184;ASN_AF=0.02;AVGPOST=0.9994;ERATE=0.0003;LDAF=0.0060;RSQ=0.9602;THETA=0.0015;VT=INDEL 249 …0.0041;AN=2184;ASN_AF=0.02;AVGPOST=0.9979;ERATE=0.0006;LDAF=0.0052;RSQ=0.8137;THETA=0.0043;VT=INDEL 262 …F=0.01;AFR_AF=0.02;AN=2184;AVGPOST=0.9973;ERATE=0.0007;LDAF=0.0068;RSQ=0.8367;THETA=0.0003;VT=INDEL 307 …F=0.01;AFR_AF=0.03;AN=2184;AVGPOST=0.9992;ERATE=0.0005;LDAF=0.0082;RSQ=0.9540;THETA=0.0017;VT=INDEL 359 …F=0.01;AFR_AF=0.03;AN=2184;AVGPOST=0.9992;ERATE=0.0003;LDAF=0.0063;RSQ=0.9442;THETA=0.0004;VT=INDEL [all …]
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/dports/biology/bio-mocha/bcftools-1.14/test/ |
H A D | reheader.1.out | 6 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 21 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 22 2 114 . TC TTCC,TTC 999 PASS INDEL;AN=4;AC=2,2 GT:DP 1/2:1 1/2:1 23 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 24 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 25 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 33 20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 34 20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,… 36 3 15 . CACA CAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 37 4 21 . ATTTTTTTTTTTTTTTC ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC 999 PASS INDEL;AN=0 … [all …]
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H A D | reheader.1.out.bcf | 6 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 21 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 22 2 114 . TC TTCC,TTC 999 PASS INDEL;AN=4;AC=2,2 GT:DP 1/2:1 1/2:1 23 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 24 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 25 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 33 20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 34 20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,… 36 3 15 . CACA CAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 37 4 21 . ATTTTTTTTTTTTTTTC ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC 999 PASS INDEL;AN=0 … [all …]
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H A D | norm.split.and.norm.out | 3 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 38 2 101 . A ATT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 39 2 101 . A AT 999 PASS INDEL;AN=4;AC=2 GT:DP 0/1:1 0/1:1 40 2 114 . T TTC 999 PASS INDEL;AN=4;AC=2 GT:DP 1/0:1 1/0:1 41 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 42 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 43 20 5 . TG CT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 44 20 5 . TGG T . PASS INDEL;AN=4;AC=2 GT:PL:DP 0/1:1,4,6:1 0/1:1,4,6:1 61 21 1 id T TTTATTA 999 PASS INDEL;AN=0;AC=0 GT:DP ./.:0 ./.:0 63 21 1 id TTTA T 999 PASS INDEL;AN=0;AC=0 GT:DP ./.:0 ./.:0 [all …]
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H A D | norm.split.out | 3 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 39 2 114 . TC TTCC 999 PASS INDEL;AN=4;AC=2 GT:DP 1/0:1 1/0:1 40 2 114 . TC TTC 999 PASS INDEL;AN=4;AC=2 GT:DP 0/1:1 0/1:1 41 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 42 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 43 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 45 20 5 . TGGG TG . PASS INDEL;AN=4;AC=2 GT:PL:DP 0/1:1,4,6:1 0/1:1,4,6:1 59 20 300 . T C 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 61 21 1 id TTTA TTTATTATTA 999 PASS INDEL;AN=0;AC=0 GT:DP ./.:0 ./.:0 63 21 1 id TTTA T 999 PASS INDEL;AN=0;AC=0 GT:DP ./.:0 ./.:0 [all …]
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H A D | norm.merge.vcf | 3 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 39 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 42 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 43 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 44 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 45 20 5 . TGGG TAC . PASS INDEL;AN=4;AC=2 GT:PL:DP 1/0:1,2,3:1 1/0:1,2,3:1 46 20 5 id0001 TGGG TG . PASS INDEL;AN=4;AC=2 GT:PL:DP 0/1:1,4,6:1 0/1:1,4,6:1 47 20 5 id0002 TGGG TGGGG . PASS INDEL;AN=4;AC=0 GT:PL:DP 0/0:1,7,10:1 0/0:1,7,10:1 48 20 5 . TGGG AC . PASS INDEL;AN=4;AC=0 GT:PL:DP 0/0:1,11,15:1 0/0:1,11,15:1 60 20 300 . A C 998 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 [all …]
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H A D | norm.vcf | 3 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 40 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4;END=114 GT:DP 1/1:1 1/1:1 41 2 114 . TC TTCC,TTC 999 PASS INDEL;AN=4;AC=2,2;END=115 GT:DP 1/2:1 1/2:1 42 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 43 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 44 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 52 20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=;END=282 GT:PL:DP ./.:0,0,0:0 ./.:0,0… 56 3 15 . CACA CAC 999 PASS INDEL;AN=0;END=18 GT:DP ./.:0 ./.:0 58 4 25 . T TT,* 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 59 4 37 . C I 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 [all …]
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H A D | norm.out | 3 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 40 2 101 . A ATT 999 PASS INDEL;AN=4;AC=4;END=101 GT:DP 1/1:1 1/1:1 41 2 114 . T TTC,TT 999 PASS INDEL;AN=4;AC=2,2;END=114 GT:DP 1/2:1 1/2:1 42 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 43 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 44 20 5 . TG CT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 53 20 273 . C CAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 56 3 17 . CA C 999 PASS INDEL;AN=0;END=18 GT:DP ./.:0 ./.:0 57 4 25 . T TT,* 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 58 4 36 . TC C,TT,TTC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 [all …]
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H A D | reheader.3.out | 26 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 38 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 39 2 114 . TC TTCC,TTC 999 PASS INDEL;AN=4;AC=2,2 GT:DP 1/2:1 1/2:1 40 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 41 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 42 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 50 20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 51 20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,… 53 3 15 . CACA CAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 54 4 21 . ATTTTTTTTTTTTTTTC ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC 999 PASS INDEL;AN=0 … [all …]
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H A D | reheader.4.out | 26 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 38 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 39 2 114 . TC TTCC,TTC 999 PASS INDEL;AN=4;AC=2,2 GT:DP 1/2:1 1/2:1 40 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 41 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 42 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 50 20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 51 20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,… 53 3 15 . CACA CAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 54 4 21 . ATTTTTTTTTTTTTTTC ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC 999 PASS INDEL;AN=0 … [all …]
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H A D | reheader.2.out | 26 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 38 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 39 2 114 . TC TTCC,TTC 999 PASS INDEL;AN=4;AC=2,2 GT:DP 1/2:1 1/2:1 40 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 41 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 42 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 50 20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 51 20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,… 53 3 15 . CACA CAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 54 4 21 . ATTTTTTTTTTTTTTTC ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC 999 PASS INDEL;AN=0 … [all …]
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H A D | reheader.vcf | 25 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 37 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 38 2 114 . TC TTCC,TTC 999 PASS INDEL;AN=4;AC=2,2 GT:DP 1/2:1 1/2:1 39 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 40 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 41 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 49 20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 50 20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,… 52 3 15 . CACA CAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 53 4 21 . ATTTTTTTTTTTTTTTC ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC 999 PASS INDEL;AN=0 … [all …]
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/dports/biology/bcftools/bcftools-1.14/test/ |
H A D | reheader.1.out | 6 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 21 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 22 2 114 . TC TTCC,TTC 999 PASS INDEL;AN=4;AC=2,2 GT:DP 1/2:1 1/2:1 23 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 24 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 25 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 33 20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 34 20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,… 36 3 15 . CACA CAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 37 4 21 . ATTTTTTTTTTTTTTTC ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC 999 PASS INDEL;AN=0 … [all …]
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H A D | reheader.1.out.bcf | 6 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 21 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 22 2 114 . TC TTCC,TTC 999 PASS INDEL;AN=4;AC=2,2 GT:DP 1/2:1 1/2:1 23 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 24 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 25 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 33 20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 34 20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,… 36 3 15 . CACA CAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 37 4 21 . ATTTTTTTTTTTTTTTC ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC 999 PASS INDEL;AN=0 … [all …]
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H A D | norm.split.and.norm.out | 3 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 38 2 101 . A ATT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 39 2 101 . A AT 999 PASS INDEL;AN=4;AC=2 GT:DP 0/1:1 0/1:1 40 2 114 . T TTC 999 PASS INDEL;AN=4;AC=2 GT:DP 1/0:1 1/0:1 41 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 42 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 43 20 5 . TG CT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 44 20 5 . TGG T . PASS INDEL;AN=4;AC=2 GT:PL:DP 0/1:1,4,6:1 0/1:1,4,6:1 61 21 1 id T TTTATTA 999 PASS INDEL;AN=0;AC=0 GT:DP ./.:0 ./.:0 63 21 1 id TTTA T 999 PASS INDEL;AN=0;AC=0 GT:DP ./.:0 ./.:0 [all …]
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H A D | norm.split.out | 3 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 39 2 114 . TC TTCC 999 PASS INDEL;AN=4;AC=2 GT:DP 1/0:1 1/0:1 40 2 114 . TC TTC 999 PASS INDEL;AN=4;AC=2 GT:DP 0/1:1 0/1:1 41 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 42 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 43 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 45 20 5 . TGGG TG . PASS INDEL;AN=4;AC=2 GT:PL:DP 0/1:1,4,6:1 0/1:1,4,6:1 59 20 300 . T C 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 61 21 1 id TTTA TTTATTATTA 999 PASS INDEL;AN=0;AC=0 GT:DP ./.:0 ./.:0 63 21 1 id TTTA T 999 PASS INDEL;AN=0;AC=0 GT:DP ./.:0 ./.:0 [all …]
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H A D | norm.merge.vcf | 3 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 39 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 42 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 43 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 44 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 45 20 5 . TGGG TAC . PASS INDEL;AN=4;AC=2 GT:PL:DP 1/0:1,2,3:1 1/0:1,2,3:1 46 20 5 id0001 TGGG TG . PASS INDEL;AN=4;AC=2 GT:PL:DP 0/1:1,4,6:1 0/1:1,4,6:1 47 20 5 id0002 TGGG TGGGG . PASS INDEL;AN=4;AC=0 GT:PL:DP 0/0:1,7,10:1 0/0:1,7,10:1 48 20 5 . TGGG AC . PASS INDEL;AN=4;AC=0 GT:PL:DP 0/0:1,11,15:1 0/0:1,11,15:1 60 20 300 . A C 998 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 [all …]
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H A D | norm.vcf | 3 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 40 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4;END=114 GT:DP 1/1:1 1/1:1 41 2 114 . TC TTCC,TTC 999 PASS INDEL;AN=4;AC=2,2;END=115 GT:DP 1/2:1 1/2:1 42 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 43 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 44 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 52 20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=;END=282 GT:PL:DP ./.:0,0,0:0 ./.:0,0… 56 3 15 . CACA CAC 999 PASS INDEL;AN=0;END=18 GT:DP ./.:0 ./.:0 58 4 25 . T TT,* 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 59 4 37 . C I 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 [all …]
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H A D | norm.out | 3 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 40 2 101 . A ATT 999 PASS INDEL;AN=4;AC=4;END=101 GT:DP 1/1:1 1/1:1 41 2 114 . T TTC,TT 999 PASS INDEL;AN=4;AC=2,2;END=114 GT:DP 1/2:1 1/2:1 42 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 43 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 44 20 5 . TG CT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 53 20 273 . C CAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 56 3 17 . CA C 999 PASS INDEL;AN=0;END=18 GT:DP ./.:0 ./.:0 57 4 25 . T TT,* 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 58 4 36 . TC C,TT,TTC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 [all …]
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H A D | reheader.4.out | 26 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 38 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 39 2 114 . TC TTCC,TTC 999 PASS INDEL;AN=4;AC=2,2 GT:DP 1/2:1 1/2:1 40 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 41 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 42 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 50 20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 51 20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,… 53 3 15 . CACA CAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 54 4 21 . ATTTTTTTTTTTTTTTC ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC 999 PASS INDEL;AN=0 … [all …]
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H A D | reheader.2.out | 26 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 38 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 39 2 114 . TC TTCC,TTC 999 PASS INDEL;AN=4;AC=2,2 GT:DP 1/2:1 1/2:1 40 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 41 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 42 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 50 20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 51 20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,… 53 3 15 . CACA CAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 54 4 21 . ATTTTTTTTTTTTTTTC ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC 999 PASS INDEL;AN=0 … [all …]
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H A D | reheader.3.out | 26 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 38 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 39 2 114 . TC TTCC,TTC 999 PASS INDEL;AN=4;AC=2,2 GT:DP 1/2:1 1/2:1 40 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 41 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1 42 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 50 20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0 51 20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,… 53 3 15 . CACA CAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0 54 4 21 . ATTTTTTTTTTTTTTTC ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC 999 PASS INDEL;AN=0 … [all …]
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/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/VQSR/ |
H A D | VQSR.AStest.indels.tranches | 4 90.00,3740,16877,0.0000,0.0000,1.1677,VQSRTrancheINDEL0.00to90.00,INDEL,8252,7426,0.8999 5 99.00,4493,22677,0.0000,0.0000,-0.7124,VQSRTrancheINDEL90.00to99.00,INDEL,8252,8169,0.9899 6 99.30,4584,23340,0.0000,0.0000,-1.1274,VQSRTrancheINDEL99.00to99.30,INDEL,8252,8194,0.9930 7 99.50,4636,23907,0.0000,0.0000,-1.6948,VQSRTrancheINDEL99.30to99.50,INDEL,8252,8210,0.9949 8 99.70,4666,24332,0.0000,0.0000,-2.8789,VQSRTrancheINDEL99.50to99.70,INDEL,8252,8227,0.9970 9 99.80,4677,24459,0.0000,0.0000,-4.1348,VQSRTrancheINDEL99.70to99.80,INDEL,8252,8235,0.9979 10 99.90,4695,24596,0.0000,0.0000,-8.5025,VQSRTrancheINDEL99.80to99.90,INDEL,8252,8243,0.9989 11 100.00,4707,24774,0.0000,0.0000,-1184.4046,VQSRTrancheINDEL99.90to100.00,INDEL,8252,8252,1.0000
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