/dports/biology/bamutil/bamUtil-1.0.15/test/expected/ |
H A D | testRecabDBSNPkeepPrev.sam.qemp | 14 rg1,26,-5,GT,99,0,20
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H A D | testRecabDBSNPkeepPrev.sam.qemp.map | 6 rg1,26,-5,GT,99,0,20
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H A D | testRecabFast.sam.qemp | 14 rg1,26,-5,GT,100,1,17
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H A D | testRecabFast.sam.qemp.map | 6 rg1,26,-5,GT,100,1,17
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/dports/biology/bbmap/bbmap/resources/ |
H A D | blacklist_nt_merged.sketch | 887 Ub<GT]@ 4861 Kk]GT]P 6931 1GT=<aFB 26768 2GT^o6Ej 41040 81GT[kL9 43913 @X8lf>GT 55493 3GT]oDQR 64535 2N[?`4GT 67300 GT]aT7^ 78198 2GT@e1G0 [all …]
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H A D | blacklist_prokprot_merged.sketch | 7694 GT>NBlf 8786 GT?g>AL 12179 1h=l<GT^ 15917 1W^758GT 17836 ?GT>L>: 19329 :6<GT[=n 20344 dR0?GT@ 41242 >UL?O?GT
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H A D | blacklist_refseq_merged.sketch | 7231 PA@GT: 27479 6Q9[\GT 35066 A^^GT=Y 42564 KhK;[GT 50665 49fo7^GT 54586 GT?Z5bG 71357 GT^^Z]S[ 74853 38SW8[GT 82953 2N[?`4GT 95001 T<4GT>Q [all …]
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H A D | blacklist_silva_merged.sketch | 4138 EUU1W[GT 4251 GT@QELMh 10197 3iiRV`GT 17568 2>GT[i2B
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/dports/biology/bcftools/bcftools-1.14/ |
H A D | NEWS | 178 - When FORMAT/GT is not present, the INFO/AF tag will be newly calculated 183 - Switch between FORMAT/GT or FORMAT/PL when one is (implicitly) requested 271 - New --use-NAIVE option for a naive DNM calling based solely on FORMAT/GT 301 bcftools query -f'[%POS %SAMPLE %GT\n]' -i'N_PASS(GT="alt")==1' 308 bcftools view -i'N_PASS(GT="alt")==1' | \ 309 bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT="alt"' 812 can be now in a file as, e.g., GT[@samples.txt]="het" 853 and missing values. New GT=ref,alt,mis etc keywords, check the documentation 861 bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]' -i'GT="alt"' file.bcf 863 bcftools view -i'GT="alt"' file.bcf -Ou | bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]' [all …]
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/dports/biology/bcftools/bcftools-1.14/misc/ |
H A D | run-roh.pl | 249 …cmd(qq[bcftools query -f'GT\\t%CHROM\\t%POS[\\t%SAMPLE\\t%GT]\\n' $file | gzip -c >> $file.txt.gz.…
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H A D | vcfutils.pl | 508 GA=>'R', GC=>'S', GT=>'K', TA=>'W', TC=>'Y', TG=>'K');
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/dports/biology/bcftools/bcftools-1.14/test/ |
H A D | ad-bias.2.out | 6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 9 22 16051347 . G C 283 . . GT:AD 1/1:2,4 0/1:20,20 0/0:43,0 11 22 16051497 . A G 362 . . GT:AD 1/1:0,8 0/1:14,20 0/0:44,0 12 22 16053659 . A C 352 . . GT:AD 1/1:0,9 1/1:0,21 0/0:30,0 13 22 16053791 . C A 287 . . GT:AD 0/1:4,4 0/1:13,16 0/0:32,0 14 22 16055942 . C T 385 . . GT:AD 1/1:0,7 1/1:0,22 0/0:31,0 15 22 16056126 . G A 263 . . GT:AD 0/1:2,6 0/1:12,16 0/0:27,0 16 22 16058415 . A G 212 . . GT:AD 0/0:9,0 1/1:0,37 0/0:35,2 17 22 16058463 . C T 136 . . GT:AD 0/1:1,8 0/0:40,0 0/0:45,0 18 22 16058758 . C A 107 . . GT:AD 1/1:2,8 0/0:19,0 0/0:34,0 [all …]
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H A D | ad-bias.2.vcf | 6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 8 22 16050159 . C T 68 . . GT:AD 0/0:4,0 0/1:6,8 0/0:26,0 9 22 16050252 . A T 85 . . GT:AD 0/0:3,0 0/1:13,13 0/0:40,0 14 22 16051968 . C A 136 . . GT:AD 0/0:4,0 0/1:11,11 0/0:13,0 18 22 16052239 . A G 172 . . GT:AD 0/0:5,0 0/1:12,17 0/0:44,0 20 22 16052618 . G A 124 . . GT:AD 0/0:7,0 0/1:29,12 0/0:41,0 24 22 16054667 . C G 179 . . GT:AD 0/0:8,0 0/1:12,15 0/0:27,0 32 22 16058070 . A G 452 . . GT:AD 1/1:0,4 1/1:0,21 1/1:0,22 33 22 16058415 . A G 212 . . GT:AD 0/0:9,0 1/1:0,37 0/0:35,2 34 22 16058463 . C T 136 . . GT:AD 0/1:1,8 0/0:40,0 0/0:45,0 [all …]
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H A D | ad-bias.vcf | 6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 8 22 16050159 . C T 68 . . GT:AD 0/0:4,0 0/1:6,8 0/0:26,0 9 22 16050252 . A T 85 . . GT:AD 0/0:3,0 0/1:13,13 0/0:40,0 10 22 16051249 . T C 32.1761 . . GT:AD 0/1:4,3 0/0:41,0 0/0:55,0 11 22 16051347 . G C 283 . . GT:AD 1/1:2,4 0/1:20,20 0/0:43,0 13 22 16051497 . A G 362 . . GT:AD 1/1:0,8 0/1:14,20 0/0:44,0 14 22 16051968 . C A 136 . . GT:AD 0/0:4,0 0/1:11,11 0/0:13,0 18 22 16052239 . A G 172 . . GT:AD 0/0:5,0 0/1:12,17 0/0:44,0 20 22 16052618 . G A 124 . . GT:AD 0/0:7,0 0/1:29,12 0/0:41,0 21 22 16053659 . A C 352 . . GT:AD 1/1:0,9 1/1:0,21 0/0:30,0 [all …]
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H A D | af-dist.vcf | 6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 11 11 2343543 . A . 999 . AN=6 GT 0/0 0/0 0/0 12 11 5464562 . C T 999 . AN=0;AC=0 GT ./. ./. ./. 13 20 76962 rs6111385 T C 999 . AN=6;AF=0.833333;AC=5 GT 0/1 1/1 1/1 14 20 126310 . ACC A 999 . AN=6;AF=0.666667;AC=4 GT 0/1 0/1 1/1 15 20 138125 rs2298108 G T 999 . AN=6;AF=0.666667;AC=4 GT 0/1 0/1 1/1 16 20 138148 rs2298109 C T 999 . AN=6;AF=0.666667;AC=4 GT 0/1 0/1 1/1 17 20 271225 . T TTTA,TA 999 . AN=6;AF=0.333333,0.333333;AC=2,2 GT 0/2 0/1 1/2 18 20 304568 . C T 999 . AN=6;AF=0.666667;AC=4 GT 0|1 0|1 1|1 19 20 326891 . A AC 999 . AN=4;AF=0.5;AC=2 GT 0|1 0|1 ./.
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H A D | annotate.multi.1.out | 6 1 752566 . G A,C,T . . ANN=GT,GC,GA
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H A D | annotate.multi.tab | 2 1 752566 G T GT
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H A D | annotate.out | 6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 32 1 3106154 indel_3106154 CAAA C 342 PASS AN=4;AC=2;INDEL GT:GQ:DP 0/1:245:32 0/1:245:32 33 1 3106154 indel_3106154 C CT 59.2 PASS AN=4;AC=2;INDEL GT:GQ:DP 0/1:245:32 0/1:245:32 34 1 3157410 indel_3157410 GA G 90.6 q10 AN=4;AC=4;INDEL GT:GQ:DP 1/1:21:21 1/1:21:21 35 1 3162006 indel_3162006 GAA G 60.2 PASS AN=4;AC=2;INDEL GT:GQ:DP 0/1:212:22 0/1:212:22 38 1 3184885 indel_3184885 TAAAA TA,T 61.5 PASS AN=4;AC=2,2;INDEL GT:GQ:DP 1/2:12:10 1/2:12:10 39 2 3199812 indel_3199812 G GTT,GT 82.7 PASS AN=4;AC=2,2;INDEL GT:GQ:DP 1/2:322:26 1/2:322:26 40 3 3212016 indel_3212016 CTT C,CT 79 PASS AN=4;AC=2,2;INDEL GT:GQ:DP 1/2:91:26 1/2:91:26 41 4 3258448 indel_3258448 TACACACAC T 59.9 PASS AN=4;AC=2;INDEL GT:GQ:DP 0/1:325:31 0/1:325:31 42 4 4000000 id1 T A,C 59.9 PASS AN=4;AC=2,0;INDEL GT:GQ:DP 0/1:325:31 0/1:325:31 [all …]
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H A D | annotate.tab | 5 2 3199812 G GTT,GT indel_3199812 . . . 1
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H A D | annotate.vcf | 5 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 24 1 3000150 . C T 59.2 PASS AN=4;AC=2 GT:GQ 0/1:245 0/1:245 25 1 3000151 . C T 59.2 PASS AN=4;AC=2 GT:DP:GQ 0/1:32:245 0/1:32:245 28 1 3106154 . CAAA C 342 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32 29 1 3106154 . C CT 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32 30 1 3157410 . GA G 90.6 q10 AN=4;AC=4 GT:GQ:DP 1/1:21:21 1/1:21:21 31 1 3162006 . GAA G 60.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:212:22 0/1:212:22 32 1 3177144 . G T 45 PASS AN=4;AC=2 GT:GQ:DP 0/0:150:30 1/1:150:30 33 1 3177144 . G . 45 PASS AN=4;AC=0 GT:GQ:DP 0/0:150:30 0/0:150:30 35 2 3199812 . G GTT,GT 82.7 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:322:26 1/2:322:26 [all …]
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H A D | annotate10.out | 10 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 15 1 3000001 . C T . . . GT:FINT:FFLT:FSTR .:.:.:. .:.:.:. 16 1 3000002 id C T 99 q99 FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999 GT:FINT:FFLT:FSTR 1|1:88,99:8.8,9… 17 1 3000003 id C T 99 q99 FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999 GT:FINT:FFLT:FSTR 1|1:88,99:8.8,9… 18 1 3000004 id C T 99 q99 FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999 GT:FINT:FFLT:FSTR 1|1:88,99:8.8,9…
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H A D | annotate10.vcf | 10 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 14 1 3000001 . C T . . . GT . . 15 1 3000002 id C T 99 q99 FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999 GT 1|1 0|1 16 1 3000003 id C T 99 q99 FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999 GT 1|1 0|1 17 1 3000004 id C T 99 q99 FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999 GT 1|1 0|1
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H A D | annotate11.out | 9 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 15 1 3000001 xx C T 11 PASS FLAG;IINT=11;IFLT=1.1;ISTR=xxx GT:FINT:FFLT:FSTR 0/0:11:1.1:xxx 0/0:11:1.1… 16 1 3000002 . C T . . . GT:FINT:FFLT:FSTR .:77:7.7:77 .:.:.:. .:.:.:. 17 1 3000003 xx C T 11 q11 FLAG;IINT=.;IFLT=.;ISTR=. GT:FINT:FFLT:FSTR 0/0:77:7.7:77 0/0:.:.:. 0/0:.:.… 18 1 3000004 xx C T 11 q11 FLAG;IINT=11;IFLT=1.1;ISTR=xxx GT:FINT:FFLT:FSTR 0/0:77:7.7:77 0/0:11:1.1:x…
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H A D | annotate11.vcf | 4 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 6 1 3000001 . C T . . . GT . . 7 1 3000002 . C T . . . GT 1|1 0 8 1 3000003 . C CT,CTT . . . GT 1|1 0 9 X 3000001 . C T . . . GT . . 10 X 3000002 . C T . . . GT 1|1 0 11 X 3000003 . C CT,CTT . . . GT 1|1 0
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H A D | annotate12.out | 9 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 17 1 3000001 xx C T 11 PASS FLAG;IINT=11;IFLT=1.1;ISTR=xxx GT:FINT:FFLT:FSTR 0/0:11:1.1:xxx 0/0:11:1.1… 18 1 3000002 . C T . . AAA=88,99 GT:BBB .:77 .:88,99 .:. 19 1 3000003 xx C T 11 q11 FLAG;IINT=.;IFLT=.;ISTR=.;AAA=88,99 GT:FINT:FFLT:FSTR:BBB 0/0:.:.:.:77 0/0:… 20 1 3000004 xx C T 11 q11 FLAG;IINT=11;IFLT=1.1;ISTR=xxx;AAA=88,99 GT:FINT:FFLT:FSTR:BBB 0/0:11:1.1:x…
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