Mercurial > repos > jjohnson > bcftools_convert_to_vcf
annotate test-data/annots.vcf @ 1:7de527c01731 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author | jjohnson |
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date | Sun, 26 Jun 2016 15:34:05 -0400 |
parents | bca07db8f55c |
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rev | line source |
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bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
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1 ##fileformat=VCFv4.1 |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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2 ##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag"> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
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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\\\\\""> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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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"> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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5 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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7 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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8 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood"> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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9 ##FILTER=<ID=q10,Description="Quality below 10"> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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10 ##FILTER=<ID=test,Description="Testing filter"> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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11 ##contig=<ID=1,assembly=b37,length=249250621> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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12 ##contig=<ID=2,assembly=b37,length=249250621> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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13 ##contig=<ID=3,assembly=b37,length=198022430> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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14 ##contig=<ID=4,assembly=b37,length=191154276> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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15 ##test=<ID=4,IE=5> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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16 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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17 ##readme=AAAAAA |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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18 ##readme=BBBBBB |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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19 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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20 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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21 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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22 ##INFO=<ID=STR,Number=1,Type=String,Description="Test string type"> |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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23 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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24 1 3000150 id1 C T 99 PASS STR=id1;AN=4;AC=0 GT:GQ 0|0:999 0|0:999 |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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25 1 3000151 id2 C T 99 PASS STR=id2;AN=4;AC=0 GT:DP:GQ 0|0:99:999 0|0:99:999 |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
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26 1 3062915 idIndel GTTT G 99 PASS DP4=1,2,3,4;AN=4;AC=0;INDEL;STR=testIndel GT:GQ:DP:GL 0|0:999:99:-99,-9,-99 0|0:999:99:-99,-9,-99 |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
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27 1 3062915 idSNP G T,C 99 PASS STR=testSNP;TEST=5;DP4=1,2,3,4;AN=3;AC=0,0 GT:TT:GQ:DP:GL 0|0:9,9:999:99:-99,-9,-99,-99,-9,-99 0:9,9:999:99:-99,-9,-99 |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
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28 1 3106154 id4 CAAA C 99 PASS STR=id4;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99 |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
changeset
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29 1 3106154 id5 C CT 99 PASS STR=id5;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99 |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
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30 1 3157410 id6 GA GC,G 99 PASS STR=id6;AN=4;AC=0 GT:GQ:DP 0|0:99:99 0|0:99:99 |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
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31 1 3162006 id7 GAA GG 99 PASS STR=id7;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99 |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
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32 1 3177144 id8 G T 99 PASS STR=id8;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99 |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
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33 1 3177144 id9 G . 99 PASS STR=id9;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99 |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
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34 1 3184885 id10 TAAAA TA,T 99 PASS STR=id10;AN=4;AC=0,0 GT:GQ:DP 0|0:99:99 0|0:99:99 |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
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35 2 3199812 id11 G GTT,GT 99 PASS STR=id11;AN=4;AC=0,0 GT:GQ:DP 0|0:999:99 0|0:999:99 |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff
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36 3 3212016 id12 CTT C,CT 99 PASS STR=id12;AN=4;AC=0,0 GT:GQ:DP 0|0:99:99 0|0:99:99 |
bca07db8f55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
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37 4 3258448 id13 TACACACAC T 99 PASS STR=id13;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99 |