Mercurial > repos > iuc > bcftools_plugin_missing2ref
annotate test-data/norm.setref.vcf @ 11:5d98fe06e4ae draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f3fe2272c80fdb749db49be689681e4d1391bee"
author | iuc |
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date | Wed, 25 Dec 2019 12:37:44 -0500 |
parents | 5e9cf5308e97 |
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rev | line source |
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5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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1 ##fileformat=VCFv4.2 |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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2 ##FILTER=<ID=PASS,Description="All filters passed"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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3 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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4 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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5 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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6 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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7 ##contig=<ID=1,length=2147483647> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
8 ##contig=<ID=2,length=2147483647> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
9 ##contig=<ID=3,length=2147483647> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
10 ##contig=<ID=4,length=2147483647> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
11 ##contig=<ID=5,length=2147483647> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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12 ##contig=<ID=20,length=2147483647> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
13 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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14 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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15 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
16 ##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
17 ##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
18 ##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
19 ##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
20 ##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
21 ##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
22 ##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
23 ##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
24 ##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
25 ##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
26 ##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
27 ##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
28 ##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
29 ##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
30 ##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
31 ##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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32 ##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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33 ##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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34 ##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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35 ##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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36 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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37 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 XY00002 |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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38 1 105 . TAACCCTAAA TAAACCCTAAA,TAA 999 PASS INDEL;AN=4;AC=2,2;DP=19 GT 1/2 1/2 |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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39 2 101 . . c 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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40 2 105 . n <DEL> 999 PASS END=112;AN=4;AC=3 GT:DP 0/1:1 1/1:1 |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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41 2 115 . t c 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1 |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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42 20 3 . c g 999 PASS INDEL;AN=4;AC=1 GT 0/0 0/1 |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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43 20 3 . gact gatg 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0 |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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44 20 10 . . . 999 PASS INDEL;AN=4;AC=1 GT 1/0 0/0 |
5e9cf5308e97
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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45 20 275 . g c,a,t,aaa 999 PASS INDEL;AN=2;AC=0,2,0,0 GT 2 2 |