Mercurial > repos > iuc > bcftools_plugin_counts

annotate test-data/view.vcf @ 6:5ad5d4243987 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 880627162bdeb854582e9f58ddab451de35feba3
author iuc
date Tue, 12 Dec 2017 14:04:56 -0500
parents 06cd2a0252dc
children
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06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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1 ##fileformat=VCFv4.1
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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2 ##reference=file:///seq/references/1000Genomes-NCBI37.fasta
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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3 ##contig=<ID=11,length=135006516>
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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4 ##contig=<ID=20,length=63025520>
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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5 ##contig=<ID=X,length=155270560>
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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6 ##contig=<ID=Y,length=59373566>
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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7 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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8 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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9 ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of reads containing spanning deletions">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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10 ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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11 ##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest contiguous homopolymer run of variant allele in either direction">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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12 ##INFO=<ID=HWE,Number=1,Type=Float,Description="Hardy-Weinberg equilibrium test (PMID:15789306)">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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13 ##INFO=<ID=ICF,Number=1,Type=Float,Description="Inbreeding coefficient F">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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14 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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15 ##INFO=<ID=IS,Number=2,Type=Float,Description="Maximum number of reads supporting an indel and fraction of indel reads">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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16 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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17 ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total mapping quality zero reads">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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18 ##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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19 ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant confidence/quality by depth">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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20 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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21 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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22 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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23 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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24 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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25 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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26 ##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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27 ##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [1e-100]">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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28 ##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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29 ##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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30 ##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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31 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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32 11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0,255,255:193:99 0/0:0,255,255:211:99 0/0:0,255,255:182:99
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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33 11 5464562 . C T 999 PASS DP=0 GT:PL:DP:GQ ./.:0,0,0:.:. ./.:0,0,0:.:. ./.:0,0,0:.:.
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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34 20 76962 rs6111385 T C 999 PASS DP4=110138,70822,421911,262673;DP=911531;Dels=0;FS=21.447;HWE=0.491006;ICF=-0.01062;MQ0=1;MQ=46;PV4=2.5e-09,0,0,1;QD=22.31 GT:PL:DP:GQ 0/1:255,0,255:193:99 1/1:255,255,0:211:99 1/1:255,255,0:182:99
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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35 20 126310 . ACC A 999 StrandBias;EndDistBias DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=6;AC=4 GT:DP:GQ:PL 0/1:117:99:255,0,132 0/1:111:99:255,0,139 1/1:78:99:255,213,0
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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36 20 138125 rs2298108 G T 999 PASS DP4=174391,20849,82080,4950;DP=286107;Dels=0;FS=3200;HWE=0.199462;ICF=0.01858;MQ0=0;MQ=46;PV4=0,0,0,1;QD=17.22;AN=6;AC=4 GT:PL:DP:GQ 0/1:135,0,163:66:99 0/1:140,0,255:71:99 1/1:255,199,0:66:99
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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37 20 138148 rs2298109 C T 999 PASS DP4=194136,45753,94945,14367;DP=356657;Dels=0;FS=3200;HWE=0.177865;ICF=0.0198;MQ0=0;MQ=47;PV4=0,0,0,1;QD=14.57;AN=6;AC=4 GT:PL:DP:GQ 0/1:195,0,255:87:99 0/1:192,0,255:82:99 1/1:255,235,0:78:99
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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38 20 271225 . T TTTA,TA 999 StrandBias DP4=29281,42401,27887,29245;DP=272732;INDEL;IS=95,0.748031;MQ=47;PV4=0,1,0,1;QD=0.0948;AN=6;AC=2,2 GT:DP:GQ:PL 0/2:33:49:151,53,203,0,52,159 0/1:51:99:255,0,213,255,255,255 1/2:47:99:255,255,255,255,0,241
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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39 20 304568 . C T 999 PASS DP4=16413,4543,945,156;DP=43557;Dels=0;FS=3200;HWE=0.076855;ICF=0.0213;MQ0=0;MQ=50;PV4=0,0,0,1;QD=15.45;AN=6;AC=4 GT:PL:DP:GQ 0|1:95,0,255:90:99 0|1:192,0,255:13:99 1|1:255,95,0:60:99
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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40 20 326891 . A AC 999 PASS DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=4;AC=2 GT:DP:GQ:PL 0|1:117:99:255,0,132 0|1:111:99:255,0,139 ./.:.:.:.,.,.
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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41 X 2928329 rs62584840 C T 999 PASS DP4=302,9137,32,1329;DP=11020;Dels=0;FS=13.38;HWE=0.284332;ICF=0.0253;MQ0=0;MQ=49;PV4=0.094,0,0,1;QD=18.61;AN=4;AC=1 GT:PL:DP:GQ 0:0,56:2:73 0:0,81:3:98 0/1:73,0,19:4:30
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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42 X 2933066 rs61746890 G C 999 PASS DP4=69865,100561,461,783;DP=173729;Dels=0;FS=10.833;MQ0=0;MQ=50;PV4=0.005,3.6e-14,0,1;QD=15.33;AN=4;AC=1 GT:PL:DP:GQ 0:0,255:39:99 0:0,255:37:99 0/1:255,255,255:62:99
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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43 X 2942109 rs5939407 T C 999 PASS DP4=23273,27816,40128,48208;DP=146673;Dels=0;FS=43.639;HWE=0.622715;ICF=-0.01176;MQ0=1;MQ=46;PV4=0.65,1,0,1;QD=14.81;AN=4;AC=3 GT:PL:DP:GQ 0:0,255:20:99 1:255,0:33:99 1/1:255,157,0:52:99
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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44 X 3048719 . T C 999 PASS DP4=13263,27466,40128,48208;DP=146673;Dels=0;FS=43.639;HWE=0.622715;ICF=-0.01176;MQ0=1;MQ=46;PV4=0.65,1,0,1;QD=14.81;AN=4;AC=3 GT:PL:DP:GQ 0:0,255:20:99 1:255,0:33:99 0|1:255,0,157:52:99
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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45 Y 8657215 . C A 999 PASS DP4=74915,114274,1948,2955;DP=195469;Dels=0;FS=3.181;MQ0=0;MQ=50;PV4=0.86,1,0,1;QD=33.77;AN=2;AC=1 GT:PL:DP:GQ 0:0,255:47:99 1:255,0:64:99 .
06cd2a0252dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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46 Y 10011673 rs78249411 G A 999 MinAB DP4=47351,30839,178796,279653;DP=550762;Dels=0;FS=41.028;MQ0=37362;MQ=26;PV4=0,0,0,1;QD=17.45;AN=2;AC=2 GT:PL:DP:GQ 1:126,101:146:37 1:95,0:130:99 .