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annotate tests/artificial-samples.vcf.in @ 5:31361191d2d2

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Uploaded tarball. Version 1.1: Stranded output, slightly different handling of minor allele ties and 0 coverage sites, revised help text, added test datasets.
author nick
date Thu, 12 Sep 2013 11:34:23 -0400
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1 ##fileformat=VCFv4.1
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2 ##comment="ARGS=-f 10 -c 10"
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3 ##comment="This is a test set of made-up sites, in this case to test the handling of multiple read groups. 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 BRAIN ARTERY THYROID
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14 # naive case
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15 chr1 0 . A G,C . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,-A=15, 0/0:1:1:+G=15,-G=15, 0/0:1:1:+C=15,-C=15,
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16 # cases all with one allele, but different minor allele numbers below threshold
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17 chr1 10 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,-A=15, 0/0:1:1:+A=15,+G=1,-A=15,-G=1, 0/0:1:1:+A=15,+G=1,-A=16,
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18 # cases with different numbers of alleles
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19 chr1 20 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,+G=1,-A=15,-G=1, 0/0:1:1:+A=17,+G=3,-A=17,-G=3, 0/0:1:1:+A=15,+G=2,-A=15,
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20 # cases where some shouldn't be printed
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21 chr1 30 . A G . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,-A=15, 0/0:1:1:+A=9,-A=8, 0/0:1:1:+A=15,-A=9,
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22 # cases with some complex pre-':' data
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23 chr1 40 . T A,G,C . . AC=1,1;AF=0.0111111111111,0.0111111111111 GT:AC:AF:NC 0/0:1:1:+T=15,-T=15, 0/0:1,1:0.0111111111111,0.0111111111111:+A=1,+T=81,-T=16,-G=2, 0/0:3,1:0.0394736842105,0.0131578947368:+C=52,+T=30,-C=17,-T=1,