Mercurial > repos > jjohnson > bcftools_plugin_missing2ref

annotate test-data/merge.4.a.vcf @ 0:ff65d6e0809b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sat, 25 Jun 2016 20:51:04 -0400
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ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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1 ##fileformat=VCFv4.1
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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2 ##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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3 ##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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4 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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5 ##INFO=<ID=TR,Number=R,Type=Float,Description="Test tag">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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6 ##INFO=<ID=TA,Number=A,Type=Float,Description="Test tag">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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7 ##INFO=<ID=TG,Number=G,Type=Float,Description="Test tag">
ff65d6e0809b 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=GT,Number=1,Type=String,Description="Genotype">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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9 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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10 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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11 ##FORMAT=<ID=XR,Number=R,Type=Integer,Description="Some description">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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12 ##FORMAT=<ID=XA,Number=A,Type=Integer,Description="Some description">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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13 ##FORMAT=<ID=XG,Number=G,Type=Integer,Description="Some description">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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14 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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15 ##FILTER=<ID=q10,Description="Quality below 10">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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16 ##FILTER=<ID=test,Description="Testing filter">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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17 ##contig=<ID=1,assembly=b37,length=249250621>
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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18 ##contig=<ID=2,assembly=b37,length=249250621>
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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19 ##contig=<ID=3,assembly=b37,length=198022430>
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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20 ##contig=<ID=4,assembly=b37,length=191154276>
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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21 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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22 ##readme=AAAAAA
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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23 ##readme=BBBBBB
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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24 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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25 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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26 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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27 ##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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28 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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29 1 3000000 id1 C CCG 59.2 PASS AN=4;AC=2;TR=1,2;TA=1;TG=1,2,3 GT:GQ:XR:XA:XG 0/1:245:0,1:1:0,1,2 0/1:245:1,2:2:0,1,2
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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30 1 3000000 . C CCG 59.2 PASS AN=4;AC=2 GT:GQ:XR:XA:XG 0/1:245:1,2:2:0,1,2 0/1:245:2,3:3:1,2,3
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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31 1 3000002 . C CCG 59.2 PASS AN=4;AC=2 GT:GQ 0/1:245 0/1:245
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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32 1 3000002 id2 C CCG 59.2 PASS AN=4;AC=2;TR=1,2;TA=1;TG=1,2,3 GT:GL:XR:XA:XG 0/1:245:.:.:. 0/1:245:.:.:.
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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33 1 3000002 id3 C CCG 59.2 PASS AN=4;AC=2;TR=1,2;TA=1;TG=1,2,3 GT:GL:XR:XA:XG 0/1:245:.:.:. 0/1:245:.