Mercurial > repos > iuc > bcftools_call

annotate test-data/mpileup.2.out @ 0:a531317a3527 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
author iuc
date Mon, 02 May 2016 17:27:10 -0400
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a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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1 ##fileformat=VCFv4.2
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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2 ##FILTER=<ID=PASS,Description="All filters passed">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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3 ##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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4 ##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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5 ##reference=file://xxx//mpileup.ref.fa.gz
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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6 ##contig=<ID=17,length=81195210>
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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7 ##ALT=<ID=X,Description="Represents allele(s) other than observed.">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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8 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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9 ##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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10 ##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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11 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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12 ##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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13 ##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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14 ##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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15 ##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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16 ##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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17 ##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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18 ##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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19 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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20 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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21 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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22 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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23 ##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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24 ##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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25 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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26 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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27 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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28 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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29 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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30 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00100 HG00101 HG00102
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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31 17 1 . A . . . END=301 GT 0/0 0/0 0/0
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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32 17 302 . T TA 488 . INDEL;IDV=7;IMF=1;DP=25;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=2,4,8,11;MQ=49 GT:PL:DP:DV 0/1:167,0,96:11:6 0/1:157,0,9:7:6 1/1:201,21,0:7:7
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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33 17 303 . G . . . END=827 GT 0/0 0/0 0/0
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34 17 828 . T C 409 . DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=2,4,8,11;MQ=60 GT:PL:DP:DV 0/1:211,0,35:12:10 0/1:116,0,91:9:5 1/1:120,12,0:4:4
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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35 17 829 . T . . . END=833 GT 0/0 0/0 0/0
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36 17 834 . G A 364 . DP=25;VDB=0.788006;SGB=-4.01214;RPB=0.999233;MQB=1;MQSB=1;BQB=0.821668;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=2,3,7,10;MQ=60 GT:PL:DP:DV 0/1:185,0,46:11:9 0/1:128,0,59:8:5 1/1:89,9,0:3:3
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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37 17 835 . T . . . END=1664 GT 0/0 0/0 0/0
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38 17 1665 . T C 3.10665 . DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;ICB=0.128205;HOB=0.0555556;AC=1;AN=6;DP4=7,11,1,1;MQ=55 GT:PL:DP:DV 0/0:0,21,185:7:0 0/0:0,27,222:9:0 0/1:35,0,51:4:2
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39 17 1666 . G . . . END=1868 GT 0/0 0/0 0/0
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40 17 1869 . A T 138 . DP=24;VDB=0.928022;SGB=-11.9537;RPB=0.984127;MQB=0.96464;MQSB=0.931547;BQB=0.359155;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,9,5,4;MQ=58 GT:PL:DP:DV 0/1:115,0,224:18:7 0/1:16,0,104:5:1 1/1:42,3,0:1:1
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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41 17 1870 . C . . . END=2040 GT 0/0 0/0 0/0
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42 17 2041 . G A 447 . DP=31;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,5,12,7;MQ=58 GT:PL:DP:DV 0/1:229,0,212:21:11 0/1:32,0,24:2:1 1/1:223,21,0:7:7
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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43 17 2042 . G . . . END=2219 GT 0/0 0/0 0/0
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44 17 2220 . G A 303 . DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,2,1,11;MQ=58 GT:PL:DP:DV 0/1:139,0,130:12:6 0/1:69,0,46:4:2 1/1:131,12,0:4:4
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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45 17 2221 . G . . . END=2563 GT 0/0 0/0 0/0
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46 17 2564 . A G 233 . DP=15;VDB=0.690812;SGB=-3.20711;RPB=0.197899;MQB=1;MQSB=1;BQB=0.965069;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=1,4,4,5;MQ=60 GT:PL:DP:DV 0/1:88,0,78:6:3 0/1:57,0,56:4:2 1/1:124,12,0:4:4
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47 17 2565 . A . . . END=3103 GT 0/0 0/0 0/0
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48 17 3104 . C T 24.2837 . DP=25;VDB=0.8;SGB=0.346553;RPB=0.717391;MQB=0.956522;MQSB=0.962269;BQB=0.978261;MQ0F=0;ICB=0.128205;HOB=0.0555556;AC=1;AN=6;DP4=8,15,2,0;MQ=58 GT:PL:DP:DV 0/0:0,48,255:16:0 0/0:0,12,144:4:0 0/1:59,0,93:5:2
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49 17 3105 . T . . . END=3586 GT 0/0 0/0 0/0
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50 17 3587 . G A 358 . DP=29;VDB=0.902044;SGB=-3.91326;RPB=0.800999;MQB=1;MQSB=1;BQB=0.156944;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=4,7,10,6;MQ=60 GT:PL:DP:DV 0/1:161,0,184:14:7 0/1:22,0,118:5:1 1/1:212,24,0:8:8
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51 17 3588 . A . . . END=3935 GT 0/0 0/0 0/0
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52 17 3936 . A G 469 . DP=37;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=5,6,6,17;MQ=56 GT:PL:DP:DV 0/1:233,0,206:20:11 0/1:77,0,58:6:4 1/1:196,24,0:8:8
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53 17 3937 . C . . . END=4101 GT 0/0 0/0 0/0