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annotate tests/real.vcf.in @ 6:df3b28364cd2

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allele-counts.{py,xml}: Add strand bias, documentation updates.
author nicksto <nmapsy@gmail.com>
date Wed, 09 Dec 2015 11:20:51 -0500
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children
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1 ##fileformat=VCFv4.1
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2 ##comment="ARGS=-r 1 -f 1 -c 10"
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3 ##comment="This is a test set of sites copied from real data. It's meant to be run with -f 1 -c 10"
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4 ##fileDate=19700101
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5 ##source=Dan
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6 ##reference=file:///scratch/dan/galaxy/galaxy-central/database/files/002/dataset_0000.dat
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7 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
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8 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
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9 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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10 ##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
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11 ##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
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12 ##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">
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13 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT THYROID
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14 chr1 246704250 . A N . . AC=1;AF=0.0333333333333 GT:AC:AF:NC 0/0:1:0.0333333333333:+A=15,+N=1,-A=14,
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15 chr1 246704257 . T N . . AC=2;AF=0.027397260274 GT:AC:AF:NC 0/0:2:0.027397260274:+T=52,+N=2,-T=19,
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16 chr1 246704268 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::+A=82,-A=22,
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17 chr1 246704269 . T . . . AC=;AF= GT:AC:AF:NC 0/0:::+T=83,-T=22,
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18 chr1 246704363 . C G,N . . AC=3,1;AF=0.0394736842105,0.0131578947368 GT:AC:AF:NC 0/0:3,1:0.0394736842105,0.0131578947368:+C=52,+G=3,+N=1,-C=20,
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19 chr1 246704437 . C A,N . . AC=5,1;AF=0.0367647058824,0.00735294117647 GT:AC:AF:NC 0/0:5,1:0.0367647058824,0.00735294117647:+C=72,-A=5,-C=58,-N=1,
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20 chr1 246707878 . G GA . . AC=6;AF=0.043795620438 GT:AC:AF:NC 0/0:6:0.043795620438:+G=90,-G=41,-GA=6,
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21 chr1 246714587 . G A . . AC=30;AF=0.41095890411 GT:AC:AF:NC 0/1:30:0.41095890411:+A=10,+G=2,-A=20,-G=41,
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22 chr1 246729215 . T G,A . . AC=1,1;AF=0.0111111111111,0.0111111111111 GT:AC:AF:NC 0/0:1,1:0.0111111111111,0.0111111111111:+A=1,+T=81,-T=7,-G=1,
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23 chr1 246729216 . T G,A . . AC=1,1;AF=0.0111111111111,0.0111111111111 GT:AC:AF:NC 0/0:1,1:0.0111111111111,0.0111111111111:+A=1,+T=81,-T=9,-G=1,
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24 chr1 246729378 . A C . . AC=7;AF=0.304347826087 GT:AC:AF:NC 0/1:7:0.304347826087:-A=16,-C=7,
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25 chr1 246729392 . A G,AG . . AC=10,1;AF=0.25,0.025 GT:AC:AF:NC 0/1:10,1:0.25,0.025:-A=29,-AG=1,-G=10,
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26 chr7 91502881 . TC T . . AC=3;AF=0.103448275862 GT:AC:AF:NC 0/0:3:0.103448275862:+T=14,-d1=3,-T=12,
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27 chr7 91502897 . C A . . AC=7;AF=0.162790697674 GT:AC:AF:NC 0/0:7:0.162790697674:+A=7,+C=17,-C=19,