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annotate tests/artificial-nofilt.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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1 ##fileformat=VCFv4.1
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2 ##comment="ARGS=-H -r 1 -f 0 -c 0"
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3 ##comment="This is a test set of made-up sites, each created in order to test certain functionality. It's meant to be run with -f 10 -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 # General note: the only data made consistent is the CHROM, POS, REF, ALT, and the variant data (after the ':'). The other stuff isn't supposed to be consistent.
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15 # Simplest case, but POS 0 and no minor allele
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16 chr1 0 . A . . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,-A=15,
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17 # Simple, normal cases of A/G variants: above/below threshold x strand bias/no strand bias (2 x 2 = 4 cases)
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18 chr1 10 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,+G=1,-A=15,-G=1,
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19 chr1 20 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,+G=1,-A=16,
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20 chr1 30 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=10,+G=2,-A=11,-G=2,
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21 chr1 40 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=11,+G=3,-A=11,
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22 # Really low coverage
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23 chr1 50 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=2,-A=1,
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24 chr1 60 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=1,+G=1,-A=1,-G=1
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25 chr1 70 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=1,+G=1,-G=2,
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26 chr1 80 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=102,+G=3,-A=2,
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27 # Very low frequency tertiary allele
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28 chr1 90 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=50,+G=5,+C=1,-A=50,-G=6,-C=1,
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29 chr1 100 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=50,+G=5,-A=50,-G=6,-C=1,
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30 # Only non-canonical alleles
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31 chr1 120 . d1 . . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+d1=15,-d1=15,
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32 # Same 4 cases, but with non-canonical major allele (d1)
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33 chr1 130 . d1 G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+d1=15,+G=1,-d1=15,-G=1,
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34 chr1 140 . d1 G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+d1=15,+G=1,-d1=16,
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35 chr1 150 . d1 G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+d1=10,+G=2,-d1=11,-G=2,
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36 chr1 160 . d1 G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+d1=11,+G=3,-d1=11,
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37 # Test case where minor allele is above threshold on only one strand because of different coverage. Also, a long decimal minor allele frequency.
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38 chr1 260 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=13,+G=7,-A=93,-G=7,
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39 # Test case where minor alleles have equal frequency: Above/below threshold, +/- strand bias
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40 chr1 300 . T G,A . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=1,+G=1,+T=38,-A=1,-G=1,-T=38,
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41 chr1 310 . T G,A . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=6,+G=6,+T=38,-A=6,-G=6,-T=38,
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42 chr1 320 . T G,A . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=6,+G=6,+T=38,-A=6,-G=6,-T=18,
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43 chr1 330 . T G,A . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=6,+G=6,+T=38,-A=1,-G=1,-T=28,
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44 chr1 340 . T G,A . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=1,+T=80,-G=1,-T=18,
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45 chr1 350 . T G,A . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=11,+T=60,-G=11,-T=18,
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46 # Case where + and - variants are interleaved with each other. Also, a long decimal result for the minor allele frequency.
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47 chr1 400 . A N . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=16,-A=16,+G=4,-G=4,
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48 # Test complex data in the ALT, INFO, and sample (before the ':') columns
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49 chr1 410 . 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=16,-G=2,
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50 chr1 420 . A . . . AC=;AF= GT:AC:AF:NC 0/0:::+A=82,-A=22,