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annotate test-data/b_out_dev/snps.vcf @ 21:0e733df972b5 draft

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author dfornika
date Tue, 12 Mar 2019 17:37:29 -0400
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21
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1 ##fileformat=VCFv4.2
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2 ##FILTER=<ID=PASS,Description="All filters passed">
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3 ##fileDate=20190312
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4 ##source=freeBayes v1.2.0-dirty
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5 ##reference=reference/ref.fa
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6 ##contig=<ID=reference,length=700>
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7 ##phasing=none
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8 ##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700"
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9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
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10 ##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
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11 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
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12 ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
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13 ##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
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14 ##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
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15 ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
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16 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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17 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
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18 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
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19 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
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20 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
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21 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
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22 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
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23 ##bcftools_viewVersion=1.9+htslib-1.9
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24 ##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Tue Mar 12 14:35:28 2019
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25 ##bcftools_annotateVersion=1.9+htslib-1.9
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26 ##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Tue Mar 12 14:35:28 2019
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27 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT b
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28 reference 4 . A T 321.326 . AB=0;AO=10;DP=10;QA=400;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:10:0:0:10:400:-36.3607,-3.0103,0