Mercurial > repos > jjohnson > bcftools_plugin_impute_info

annotate test-data/view.GL.vcf @ 1:f125988aa89e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sun, 26 Jun 2016 15:40:03 -0400
parents 8dcc53e60847
children
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8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
1 ##fileformat=VCFv4.1
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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2 ##FILTER=<ID=PASS,Description="All filters passed">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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3 ##reference=file:///seq/references/1000Genomes-NCBI37.fasta
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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4 ##contig=<ID=11,length=135006516>
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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5 ##contig=<ID=20,length=63025520>
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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6 ##contig=<ID=X,length=155270560>
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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7 ##contig=<ID=Y,length=59373566>
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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8 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="List of Phred-scaled genotype likelihoods">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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9 ##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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10 ##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [1e-100]">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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11 ##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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12 ##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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13 ##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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14 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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15 11 2343543 . A . 999 PASS . GL 0,-25.5,-25.5 0,-25.5,-25.5 0,-25.5,-25.5
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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16 11 5464562 . C T 999 PASS . GL 0,0,0 0,0,0 0,0,0
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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17 20 76962 rs6111385 T C 999 PASS . GL -25.5,0,-25.5 -25.5,-25.5,0 -25.5,-25.5,0
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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18 20 126310 . ACC A 999 StrandBias;EndDistBias . GL -25.5,0,-13.2 -25.5,0,-13.9 -25.5,-21.3,0
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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19 20 138125 rs2298108 G T 999 PASS . GL -13.5,0,-16.3 -14,0,-25.5 -25.5,-19.9,0
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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20 20 138148 rs2298109 C T 999 PASS . GL -19.5,0,-25.5 -19.2,0,-25.5 -25.5,-23.5,0
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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21 20 271225 . T TTTA,TA 999 StrandBias . GL -15.1,-5.3,-20.3,0,-5.2,-15.9 -25.5,0,-21.3,-25.5,-25.5,-25.5 -25.5,-25.5,-25.5,-25.5,0,-24.1
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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22 20 304568 . C T 999 PASS . GL -9.5,0,-25.5 -19.2,0,-25.5 -25.5,-9.5,0
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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23 20 326891 . A AC 999 PASS . GL -25.5,0,-13.2 -25.5,0,-13.9 .,.,.
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
24 X 2928329 rs62584840 C T 999 PASS . GL 0,-5.6 0,-8.1 -7.3,0,-1.9
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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25 X 2933066 rs61746890 G C 999 PASS . GL 0,-25.5 0,-25.5 -25.5,-25.5,-25.5
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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26 X 2942109 rs5939407 T C 999 PASS . GL 0,-25.5 -25.5,0 -25.5,-15.7,0
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
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27 X 3048719 . T C 999 PASS . GL 0,-25.5 -25.5,0 -25.5,0,-15.7
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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28 Y 8657215 . C A 999 PASS . GL 0,-25.5 -25.5,0 .
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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29 Y 10011673 rs78249411 G A 999 MinAB . GL -12.6,-10.1 -9.5,0 .