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annotate tests/errors.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, each created in order to test a certain type of error handling. 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 # A correct control
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15 chr1 0 . A . . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,-A=15,
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16 # List some bases more than once
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17 chr1 0 . A . . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,-A=15,+A=12,
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18 # Comma omissions
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19 chr1 0 . A . . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,-A=15
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20 chr1 0 . A . . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15-A=15,
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21 chr1 0 . A . . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,+G=1,+C=1,-A=15,-G=1,
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22 chr1 0 . A . . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,+G=1+C=1,-A=15,-G=1,
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23 # Wrong number of sample columns
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24 chr1 0 . A . . . AC=;AF= GT:AC:AF:NC 0/0:1:1:+A=15,-A=15, 0/0:1:1:+A=15,-A=15,
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25 chr1 0 . A . . . AC=;AF= GT:AC:AF:NC