Mercurial > repos > jjohnson > bcftools_convert_to_vcf

annotate test-data/concat.1.a.vcf @ 0:bca07db8f55c 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 20:47:33 -0400
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bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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1 ##fileformat=VCFv4.0
bca07db8f55c 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=Fail,Description="Test">
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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3 ##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
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4 ##INFO=<ID=XX,Number=1,Type=Integer,Description="Test">
bca07db8f55c 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=DP,Number=1,Type=Integer,Description="Total Depth">
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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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
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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
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8 ##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
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9 ##contig=<ID=2,length=62435964>
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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10 ##contig=<ID=1,length=62435964>
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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11 ##samtoolsVersion=0.2.0-rc10+htslib-0.2.0-rc10
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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12 ##samtoolsCommand=samtools mpileup -t INFO/DPR -C50 -pm3 -F0.2 -d10000 -ug -r 1:1-1000000 -b mpileup.2014-07-03//lists/chr1-pooled.list -f human_g1k_v37.fasta
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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13 ##ALT=<ID=X,Description="Represents allele(s) other than observed.">
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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14 ##bcftools_callVersion=0.2.0-rc10-2-gcd94fde+htslib-0.2.0-rc10
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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15 ##bcftools_callCommand=call -vm -f GQ -S mpileup.2014-07-03//pooled/1/1:1-1000000.samples -
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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16 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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17 1 100 . GTTT G 1806 q10 XX=11;DP=35 GT:GQ:DP 0/1:409:35
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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18 1 110 . C T,G 1792 Fail DP=32 GT:GQ:DP 0/1:245:32
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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19 1 110 . CAAA C 1792 Fail DP=32 GT:GQ:DP 0/1:245:32
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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20 1 120 . GA G 628 q10 DP=21 GT:GQ:DP 1/1:21:21
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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21 1 130 . G T 1016 Fail DP=22 GT:GQ:DP 0/1:212:22
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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22 1 130 . GAA GG 1016 Fail DP=22 GT:GQ:DP 0/1:212:22
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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23 1 140 . GT G 727 PASS DP=30 GT:GQ:DP 0/1:150:30
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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24 1 150 . TAAAA TA,T 246 Fail DP=10 GT:GQ:DP 1/2:12:10
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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25 1 160 . TAAAA TA,T 246 Fail DP=10 GT:GQ:DP 1/2:12:10
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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26 2 100 . GTTT G 1806 q10 DP=35 GT:GQ:DP 0/1:409:35
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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27 2 110 . CAAA C 1792 PASS DP=32 GT:GQ:DP 0/1:245:32
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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28 2 120 . GA G 628 q10 DP=21 GT:GQ:DP 1/1:21:21
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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29 2 130 . GAA G 1016 PASS DP=22 GT:GQ:DP 0/1:212:22
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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30 2 140 . GT G 727 PASS DP=30 GT:GQ:DP 0/1:150:30
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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31 2 150 . TAAAA TA,T 246 PASS DP=10 GT:GQ:DP 1/2:12:10
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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32 2 160 . TAAAA TA,TC,T 246 PASS DP=10 GT:GQ:DP 0/2:12:10