Mercurial > repos > galaxyp > custom_pro_db
diff test-data/hg19/test1.vcf @ 1:ad130eaa3a05 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e025f5b4d590c44537cf0702e2fb040a28f98fec
| author | galaxyp |
|---|---|
| date | Fri, 12 May 2017 13:17:40 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19/test1.vcf Fri May 12 13:17:40 2017 -0400 @@ -0,0 +1,87 @@ +##fileformat=VCFv4.1 +##samtoolsVersion=0.1.17 (r973:277) +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads"> +##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same"> +##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)"> +##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)"> +##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies"> +##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3"> +##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint"> +##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio"> +##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio"> +##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2."> +##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples."> +##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2."> +##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2."> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases"> +##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value"> +##FORMAT=<ID=PL,Number=-1,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test +chr1 32386425 . T C 24 . DP=3;AF1=1;AC1=2;DP4=0,0,0,3;MQ=50;FQ=-36 GT:PL:GQ 1/1:56,9,0:15 +chr1 32507666 . G T 6.2 . DP=5;AF1=0.4999;AC1=1;DP4=3,0,2,0;MQ=50;FQ=8.65;PV4=1,0.062,1,0.36 GT:PL:GQ 0/1:35,0,78:36 +chr1 32524459 . A C 3.54 . DP=5;AF1=0.4998;AC1=1;DP4=1,2,0,2;MQ=50;FQ=5.47;PV4=1,0.0021,1,1 GT:PL:GQ 0/1:31,0,98:30 +chr1 32622505 . G A 101 . DP=18;AF1=0.5;AC1=1;DP4=10,0,5,2;MQ=50;FQ=104;PV4=0.15,0.0055,1,0.0075 GT:PL:GQ 0/1:131,0,162:99 +chr12 25357574 . CAA C 109 . INDEL;DP=5;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-46.5 GT:PL:GQ 1/1:149,12,0:21 +chr12 25357628 . TA T 53.4 . INDEL;DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-43.5 GT:PL:GQ 1/1:93,9,0:16 +chr12 25358650 . A T 73 . DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-72 GT:PL:GQ 1/1:106,45,0:87 +chr12 25358662 . CTTTTTTTT CTTTTTT,CTTTTTTT 31.6 . INDEL;DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-52.5 GT:PL:GQ 1/1:96,42,24,91,0,64:33 +chr12 25358943 . T C 67.1 . DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48 GT:PL:GQ 1/1:100,21,0:39 +chr12 25358969 . T G 36.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:69,12,0:21 +chr12 25359352 . G A 172 . DP=16;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69 GT:PL:GQ 1/1:205,42,0:81 +chr12 25359464 . TAA TA 123 . INDEL;DP=26;AF1=1;AC1=2;DP4=0,0,26,0;MQ=50;FQ=-113 GT:PL:GQ 1/1:164,78,0:99 +chr12 25360138 . T C 169 . DP=21;AF1=1;AC1=2;DP4=0,0,19,0;MQ=50;FQ=-84 GT:PL:GQ 1/1:202,57,0:99 +chr12 25361091 . T C 93 . DP=15;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69 GT:PL:GQ 1/1:126,42,0:81 +chr12 25362217 . A G 179 . DP=20;AF1=1;AC1=2;DP4=0,0,20,0;MQ=50;FQ=-87 GT:PL:GQ 1/1:212,60,0:99 +chr12 25362465 . G A 38.3 . DP=18;AF1=1;AC1=2;DP4=0,0,5,0;MQ=50;FQ=-42 GT:PL:GQ 1/1:71,15,0:27 +chr12 25362552 . A C 156 . DP=10;AF1=1;AC1=2;DP4=0,0,10,0;MQ=50;FQ=-57 GT:PL:GQ 1/1:189,30,0:57 +chr12 25364387 . T C 21 . DP=7;AF1=0.5;AC1=1;DP4=3,1,0,2;MQ=50;FQ=24;PV4=0.4,1,1,1 GT:PL:GQ 0/1:51,0,112:54 +chr12 25368462 . C T 112 . DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48 GT:PL:GQ 1/1:145,21,0:39 +chr17 37866082 . G A 141 . DP=45;AF1=0.5;AC1=1;DP4=25,0,20,0;MQ=50;FQ=144;PV4=1,1,1,1 GT:PL:GQ 0/1:171,0,180:99 +chr17 37870047 . A G 30 . DP=3;AF1=0.5008;AC1=1;DP4=0,1,2,0;MQ=50;FQ=-4.12;PV4=0.33,1,1,1 GT:PL:GQ 0/1:60,0,25:28 +chr17 37879466 . G A 7.8 . DP=3;AF1=0.5001;AC1=1;DP4=1,0,1,1;MQ=50;FQ=4.79;PV4=1,0.064,1,1 GT:PL:GQ 0/1:37,0,31:34 +chr17 37885332 . G A 83.5 . DP=4;AF1=1;AC1=2;DP4=0,0,0,4;MQ=50;FQ=-39 GT:PL:GQ 1/1:116,12,0:21 +chr17 37898543 . T C 165 . DP=26;AF1=1;AC1=2;DP4=0,0,21,0;MQ=50;FQ=-90 GT:PL:GQ 1/1:198,63,0:99 +chr17 7530271 . C T 143 . DP=71;AF1=0.5;AC1=1;DP4=32,2,34,0;MQ=50;FQ=146;PV4=0.49,4.1e-06,1,1 GT:PL:GQ 0/1:173,0,238:99 +chr17 7572657 . G T 225 . DP=122;AF1=0.5;AC1=1;DP4=59,0,58,3;MQ=50;FQ=163;PV4=0.24,0.06,1,0.27 GT:PL:GQ 0/1:255,0,190:99 +chr17 7591866 . G T 45 . DP=14;AF1=0.5;AC1=1;DP4=10,0,4,0;MQ=50;FQ=48;PV4=1,0.062,1,0.01 GT:PL:GQ 0/1:75,0,162:78 +chr17 7606153 . C T 74 . DP=16;AF1=0.5;AC1=1;DP4=10,0,5,0;MQ=50;FQ=77;PV4=1,0.12,1,1 GT:PL:GQ 0/1:104,0,165:99 +chr2 48010558 . C A 12.3 . DP=7;AF1=0.5002;AC1=1;DP4=1,0,2,0;MQ=50;FQ=5.23;PV4=1,0.065,1,1 GT:PL:GQ 0/1:42,0,31:34 +chr2 48016554 . T C 32 . DP=4;AF1=0.5;AC1=1;DP4=1,1,2,0;MQ=50;FQ=20.9;PV4=1,1,1,0.21 GT:PL:GQ 0/1:62,0,48:51 +chr2 48018081 . A G 77 . DP=6;AF1=0.501;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-4.75;PV4=1,1,1,0.34 GT:PL:GQ 0/1:107,0,24:27 +chr2 48018221 . C T 22 . DP=7;AF1=0.5;AC1=1;DP4=5,0,2,0;MQ=50;FQ=25;PV4=1,1,1,1 GT:PL:GQ 0/1:52,0,116:55 +chr2 48027990 . G T 122 . DP=17;AF1=0.5;AC1=1;DP4=7,0,9,0;MQ=50;FQ=104;PV4=1,1,1,0.039 GT:PL:GQ 0/1:152,0,131:99 +chr2 48030458 . G C 105 . DP=4;AF1=1;AC1=2;DP4=0,0,3,1;MQ=50;FQ=-39 GT:PL:GQ 1/1:137,12,0:21 +chr5 112154737 . CT C 29 . INDEL;DP=5;AF1=0.5;AC1=1;DP4=3,0,2,0;MQ=50;FQ=32;PV4=1,1,1,0.0012 GT:PL:GQ 0/1:59,0,85:62 +chr5 112162854 . T C 60 . DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-36 GT:PL:GQ 1/1:92,9,0:16 +chr5 112164561 . G A 87.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:120,12,0:21 +chr5 112175639 . C T 31 . DP=4;AF1=0.5;AC1=1;DP4=2,0,2,0;MQ=50;FQ=31.5;PV4=1,0.21,1,1 GT:PL:GQ 0/1:61,0,62:61 +chr5 112175897 . GAA GA 7.8 . INDEL;DP=7;AF1=0.5;AC1=1;DP4=4,0,3,0;MQ=50;FQ=10.4;PV4=1,0.0018,1,0.33 GT:PL:GQ 0/1:37,0,97:39 +chr5 112176559 . T G 72 . DP=11;AF1=1;AC1=2;DP4=0,0,8,0;MQ=50;FQ=-51 GT:PL:GQ 1/1:105,24,0:45 +chr5 112176756 . T A 143 . DP=10;AF1=1;AC1=2;DP4=0,0,9,0;MQ=50;FQ=-54 GT:PL:GQ 1/1:176,27,0:51 +chr5 112180015 . C A 123 . DP=11;AF1=0.5;AC1=1;DP4=3,0,8,0;MQ=50;FQ=40;PV4=1,1,1,1 GT:PL:GQ 0/1:153,0,67:70 +chr5 112204170 . G A 112 . DP=5;AF1=1;AC1=2;DP4=0,0,2,2;MQ=50;FQ=-39 GT:PL:GQ 1/1:144,12,0:21 +chr7 140043303 . C T 88 . DP=18;AF1=0.5;AC1=1;DP4=11,0,7,0;MQ=50;FQ=91;PV4=1,0.00034,1,0.42 GT:PL:GQ 0/1:118,0,167:99 +chr7 140065806 . T C 38.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:71,12,0:21 +chr7 140065845 . C A 44.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:77,12,0:21 +chr7 140152904 . CAAAA CAAAAA 41.5 . INDEL;DP=42;AF1=0.5;AC1=1;DP4=23,0,16,0;MQ=50;FQ=44.2;PV4=1,1,1,1 GT:PL:GQ 0/1:79,0,91:82 +chr7 140153495 . G T 140 . DP=52;AF1=0.5;AC1=1;DP4=28,0,22,0;MQ=50;FQ=143;PV4=1,0.082,1,0.00038 GT:PL:GQ 0/1:170,0,184:99 +chr7 140158851 . C G 153 . DP=36;AF1=1;AC1=2;DP4=1,0,33,0;MQ=50;FQ=-102;PV4=1,1,1,1 GT:PL:GQ 1/1:186,75,0:99 +chr7 140244560 . C T 78 . DP=6;AF1=0.5013;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-5.45;PV4=1,1,1,1 GT:PL:GQ 0/1:108,0,23:26 +chr7 140406430 . T A 8.64 . DP=27;AF1=0.5;AC1=1;DP4=19,0,6,0;MQ=50;FQ=11.3;PV4=1,1,1,0.00021 GT:PL:GQ 0/1:38,0,167:40 +chr7 140406436 . A G 4.77 . DP=14;AF1=0.4999;AC1=1;DP4=12,0,2,0;MQ=50;FQ=6.99;PV4=1,1,1,0.08 GT:PL:GQ 0/1:33,0,170:33 +chr7 140424582 . G C 18.1 . DP=5;AF1=0.5;AC1=1;DP4=0,2,1,2;MQ=50;FQ=20.4;PV4=1,0.00086,1,1 GT:PL:GQ 0/1:48,0,56:50 +chr7 140426098 . G A 10.2 . DP=3;AF1=1;AC1=2;DP4=0,0,2,0;MQ=50;FQ=-33 GT:PL:GQ 1/1:41,6,0:8 +chr7 140702871 . G A 77.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:110,12,0:21 +chr7 140706061 . G T 119 . DP=74;AF1=0.5;AC1=1;DP4=45,0,22,0;MQ=50;FQ=122;PV4=1,1,1,1 GT:PL:GQ 0/1:149,0,178:99 +chr7 140706157 . G T 42 . DP=25;AF1=0.5;AC1=1;DP4=13,0,9,0;MQ=50;FQ=45;PV4=1,5.7e-11,1,0.013 GT:PL:GQ 0/1:72,0,170:75 +chr9 86583076 . C T 64 . DP=17;AF1=0.5;AC1=1;DP4=5,0,11,0;MQ=50;FQ=66;PV4=1,1.4e-08,1,1 GT:PL:GQ 0/1:94,0,100:96 +chr9 86593314 . G C 186 . DP=203;AF1=0.5;AC1=1;DP4=100,0,99,0;MQ=50;FQ=186;PV4=1,1,1,0.072 GT:PL:GQ 0/1:216,0,216:99 +chr9 86595070 . C T 140 . DP=93;AF1=0.5;AC1=1;DP4=53,0,38,0;MQ=50;FQ=143;PV4=1,0.43,1,1 GT:PL:GQ 0/1:170,0,188:99 +chr9 86595498 . G A 66 . DP=128;AF1=0.5;AC1=1;DP4=50,2,76,0;MQ=50;FQ=69;PV4=0.16,6e-81,1,1 GT:PL:GQ 0/1:96,0,225:99