Mercurial > repos > iuc > snpsift

annotate test-data/extFields_test3_in.vcf @ 5:09d6806c609e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
author iuc
date Wed, 18 Apr 2018 07:28:51 -0400
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5
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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1 ##fileformat=VCFv4.2
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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2 ##fileDate=20180328
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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3 ##source=freeBayes v1.1.0-46-g8d2b3a0-dirty
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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4 ##reference=localref.fa
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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5 ##contig=<ID=U00096,length=4639675>
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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6 ##phasing=none
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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7 ##commandline="freebayes --region U00096:0..4639675 --bam b_0.bam --bam b_1.bam --bam b_2.bam --bam b_3.bam --bam b_4.bam --bam b_5.bam --bam b_6.bam --bam b_7.bam --bam b_8.bam --bam b_9.bam --bam b_10.bam --bam b_11.bam --bam b_12.bam --fasta-reference localref.fa --vcf ./vcf_output/part_U00096:0..4639675.vcf --theta 0.001 --ploidy 1 -K -m 20 -q 20 -R 0 -Y 0 -e 1000 -F 0.2 -C 2 -G 1 --min-coverage 0 --min-alternate-qsum 0"
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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8 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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10 ##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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11 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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12 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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13 ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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14 ##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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15 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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16 ##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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17 ##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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18 ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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19 ##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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20 ##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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21 ##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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22 ##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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23 ##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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24 ##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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25 ##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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26 ##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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27 ##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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28 ##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">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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29 ##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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30 ##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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31 ##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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32 ##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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33 ##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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34 ##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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35 ##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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36 ##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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37 ##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without.">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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38 ##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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39 ##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
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40 ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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41 ##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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42 ##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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43 ##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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44 ##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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45 ##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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46 ##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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47 ##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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48 ##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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49 ##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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50 ##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">
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51 ##INFO=<ID=technology.ILLUMINA,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from ILLUMINA">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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52 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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53 ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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54 ##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">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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55 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
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56 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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57 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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58 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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59 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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60 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
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61 ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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62 ##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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63 ##SnpEffCmd="SnpEff -i vcf -o vcf -formatEff U00096 /galaxy-repl/main/files/024/679/dataset_24679041.dat "
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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64 ##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype [ | ERRORS | WARNINGS ] )' ">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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65 ##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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66 ##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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diff changeset
67 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B C
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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68 U00096 1518079 . T G 1.82951E-13 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=13;CIGAR=1X;DP=170;DPB=170;DPRA=3.80208;EPP=7.18621;EPPR=80.8099;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=13;NUMALT=1;ODDS=31.1313;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=314;QR=4764;RO=157;RPL=9;RPP=7.18621;RPPR=8.0033;RPR=4;RUN=1;SAF=13;SAP=31.2394;SAR=0;SRF=63;SRP=16.3019;SRR=94;TYPE=snp;technology.ILLUMINA=1;EFF=synonymous_variant(LOW|SILENT|ggT/ggG|p.Gly343Gly/c.1029T>G|345|curA|protein_coding|CODING|b1449|1|G),upstream_gene_variant(MODIFIER||2861|c.-2861A>C|31|yncL|protein_coding|CODING|b4598||G),upstream_gene_variant(MODIFIER||1724|c.-1724A>C|149|ydcZ|protein_coding|CODING|b1447||G),upstream_gene_variant(MODIFIER||1209|c.-1209A>C|172|mnaT|protein_coding|CODING|b1448||G),upstream_gene_variant(MODIFIER||207|c.-207T>G|221|mcbR|protein_coding|CODING|b1450||G),upstream_gene_variant(MODIFIER||3252|c.-3252T>G|353|yncE|protein_coding|CODING|b1452||G),downstream_gene_variant(MODIFIER||4499|c.*4499T>G|264|ydcV|protein_coding|CODING|b1443||G),downstream_gene_variant(MODIFIER||3053|c.*3053T>G|474|patD|protein_coding|CODING|b1444||G),downstream_gene_variant(MODIFIER||2493|c.*2493T>G|57|ydcX|protein_coding|CODING|b1445||G),downstream_gene_variant(MODIFIER||2174|c.*2174T>G|77|ydcY|protein_coding|CODING|b1446||G),downstream_gene_variant(MODIFIER||908|c.*908A>C|700|yncD|protein_coding|CODING|b1451||G),downstream_gene_variant(MODIFIER||4426|c.*4426A>C|499|ansP|protein_coding|CODING|b1453||G) GT:DP:AD:RO:QR:AO:QA:GL 0:4:3,1:3:86:1:20:0,-6.02567 0:8:8,0:8:254:0:0:0,-23.1652 0:13:12,1:12:353:1:20:0,-30.048
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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69 U00096 1518212 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=2;CIGAR=1X;DP=489;DPB=489;DPRA=0.250522;EPP=3.0103;EPPR=61.9789;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=13;NUMALT=1;ODDS=87.0721;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=18812;RO=487;RPL=0;RPP=7.35324;RPPR=20.7076;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=285;SRP=33.7275;SRR=202;TYPE=snp;technology.ILLUMINA=1;EFF=upstream_gene_variant(MODIFIER||2994|c.-2994A>T|31|yncL|protein_coding|CODING|b4598||A),upstream_gene_variant(MODIFIER||1857|c.-1857A>T|149|ydcZ|protein_coding|CODING|b1447||A),upstream_gene_variant(MODIFIER||1342|c.-1342A>T|172|mnaT|protein_coding|CODING|b1448||A),upstream_gene_variant(MODIFIER||74|c.-74T>A|221|mcbR|protein_coding|CODING|b1450||A),upstream_gene_variant(MODIFIER||3119|c.-3119T>A|353|yncE|protein_coding|CODING|b1452||A),downstream_gene_variant(MODIFIER||4632|c.*4632T>A|264|ydcV|protein_coding|CODING|b1443||A),downstream_gene_variant(MODIFIER||3186|c.*3186T>A|474|patD|protein_coding|CODING|b1444||A),downstream_gene_variant(MODIFIER||2626|c.*2626T>A|57|ydcX|protein_coding|CODING|b1445||A),downstream_gene_variant(MODIFIER||2307|c.*2307T>A|77|ydcY|protein_coding|CODING|b1446||A),downstream_gene_variant(MODIFIER||124|c.*124T>A|345|curA|protein_coding|CODING|b1449||A),downstream_gene_variant(MODIFIER||775|c.*775A>T|700|yncD|protein_coding|CODING|b1451||A),downstream_gene_variant(MODIFIER||4293|c.*4293A>T|499|ansP|protein_coding|CODING|b1453||A),intergenic_region(MODIFIER|||n.1518212T>A|||||||A) GT:DP:AD:RO:QR:AO:QA:GL 0:10:8,2:8:312:2:78:0,-21.0397 0:9:9,0:9:356:0:0:0,-32.4019 0:65:65,0:65:2497:0:0:0,-224.912
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
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70 U00096 1523784 . G A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=17;CIGAR=1X;DP=283;DPB=283;DPRA=2.07026;EPP=39.9253;EPPR=120.564;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=13;NUMALT=1;ODDS=63.7167;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=375;QR=9560;RO=266;RPL=0;RPP=39.9253;RPPR=6.9614;RPR=17;RUN=1;SAF=0;SAP=39.9253;SAR=17;SRF=189;SRP=105.412;SRR=77;TYPE=snp;technology.ILLUMINA=1;EFF=missense_variant(MODERATE|MISSENSE|tCg/tTg|p.Ser74Leu/c.221C>T|499|ansP|protein_coding|CODING|b1453|1|A),upstream_gene_variant(MODIFIER||2695|c.-2695C>T|700|yncD|protein_coding|CODING|b1451||A),upstream_gene_variant(MODIFIER||487|c.-487G>A|205|yncG|protein_coding|CODING|b1454||A),upstream_gene_variant(MODIFIER||1180|c.-1180G>A|70|yncH|protein_coding|CODING|b1455||A),upstream_gene_variant(MODIFIER||2142|c.-2142G>A|678|rhsE|protein_coding|CODING|b1456||A|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||4162|c.-4162G>A|160|ydcD|protein_coding|CODING|b1457||A),upstream_gene_variant(MODIFIER||4826|c.-4826G>A|350|yncI|protein_coding|CODING|b1459||A|WARNING_TRANSCRIPT_NO_START_CODON),downstream_gene_variant(MODIFIER||4833|c.*4833G>A|221|mcbR|protein_coding|CODING|b1450||A),downstream_gene_variant(MODIFIER||1392|c.*1392G>A|353|yncE|protein_coding|CODING|b1452||A) GT:DP:AD:RO:QR:AO:QA:GL 0:9:9,0:9:327:0:0:0,-29.7663 0:16:16,0:16:580:0:0:0,-52.5218 0:26:24,2:24:916:2:44:0,-78.566
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
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71 U00096 1524994 . CTTT CT 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=2;CIGAR=1M2D1M;DP=302;DPB=301;DPRA=0.368601;EPP=7.35324;EPPR=19.6872;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=13;NUMALT=1;ODDS=68.2413;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=11356;RO=300;RPL=1;RPP=3.0103;RPPR=19.6872;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=170;SRP=14.5915;SRR=130;TYPE=del;technology.ILLUMINA=1;EFF=frameshift_variant(HIGH||ttc/|p.Phe12fs/c.34_35delTT|70|yncH|protein_coding|CODING|b1455|1|CT|INFO_REALIGN_3_PRIME),upstream_gene_variant(MODIFIER||3907|c.-3908_-3907delAA|700|yncD|protein_coding|CODING|b1451||CT),upstream_gene_variant(MODIFIER||992|c.-993_-992delAA|499|ansP|protein_coding|CODING|b1453||CT),upstream_gene_variant(MODIFIER||930|c.-930_-929delTT|678|rhsE|protein_coding|CODING|b1456||CT|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||2950|c.-2950_-2949delTT|160|ydcD|protein_coding|CODING|b1457||CT),upstream_gene_variant(MODIFIER||3614|c.-3614_-3613delTT|350|yncI|protein_coding|CODING|b1459||CT|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||4844|c.-4844_-4843delTT|378|ydcC|protein_coding|CODING|b1460||CT),downstream_gene_variant(MODIFIER||2604|c.*2604_*2605delTT|353|yncE|protein_coding|CODING|b1452||CT),downstream_gene_variant(MODIFIER||108|c.*108_*109delTT|205|yncG|protein_coding|CODING|b1454||CT);LOF=(yncH|b1455|1|1.00) GT:DP:AD:RO:QR:AO:QA:GL 0:6:6,0:6:209:0:0:0,-19.1481 0:9:7,2:7:271:2:71:0,-18.0127 0:26:26,0:26:1011:0:0:0,-91.2905
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
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72 U00096 1525214 . T A 0.0 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=2;CIGAR=1X;DP=325;DPB=325;DPRA=0.264151;EPP=3.0103;EPPR=21.8947;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=13;NUMALT=1;ODDS=54.1924;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=12493;RO=323;RPL=2;RPP=7.35324;RPPR=11.2458;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=153;SRP=4.9532;SRR=170;TYPE=snp;technology.ILLUMINA=1;EFF=upstream_gene_variant(MODIFIER||4125|c.-4125A>T|700|yncD|protein_coding|CODING|b1451||A),upstream_gene_variant(MODIFIER||1210|c.-1210A>T|499|ansP|protein_coding|CODING|b1453||A),upstream_gene_variant(MODIFIER||712|c.-712T>A|678|rhsE|protein_coding|CODING|b1456||A|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||2732|c.-2732T>A|160|ydcD|protein_coding|CODING|b1457||A),upstream_gene_variant(MODIFIER||3396|c.-3396T>A|350|yncI|protein_coding|CODING|b1459||A|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||4626|c.-4626T>A|378|ydcC|protein_coding|CODING|b1460||A),downstream_gene_variant(MODIFIER||2822|c.*2822T>A|353|yncE|protein_coding|CODING|b1452||A),downstream_gene_variant(MODIFIER||326|c.*326T>A|205|yncG|protein_coding|CODING|b1454||A),downstream_gene_variant(MODIFIER||38|c.*38T>A|70|yncH|protein_coding|CODING|b1455||A),intergenic_region(MODIFIER|||n.1525214T>A|||||||A) GT:DP:AD:RO:QR:AO:QA:GL 0:6:6,0:6:232:0:0:0,-21.246 0:11:11,0:11:433:0:0:0,-39.3229 0:38:38,0:38:1471:0:0:0,-132.652
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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73 U00096 1525377 . AGG AGGG,AGT 5.68956E-14 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=13;AO=2,3;CIGAR=1M1I2M,2M1X;DP=621;DPB=621.667;DPRA=0.196399,1.09363;EPP=3.0103,3.73412;EPPR=17.9768;GTI=0;LEN=1,1;MEANALT=2,1.5;MQM=60,60;MQMR=60;NS=13;NUMALT=2;ODDS=87.143;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=71,97;QR=23655;RO=613;RPL=2,1;RPP=7.35324,3.73412;RPPR=192.035;RPR=0,2;RUN=1,1;SAF=1,2;SAP=3.0103,3.73412;SAR=1,1;SRF=366;SRP=53.1738;SRR=247;TYPE=ins,snp;technology.ILLUMINA=1,1;EFF=upstream_gene_variant(MODIFIER||4290|c.-4290C>A|700|yncD|protein_coding|CODING|b1451||AGT),upstream_gene_variant(MODIFIER||4291|c.-4291_-4290insC|700|yncD|protein_coding|CODING|b1451||AGGG),upstream_gene_variant(MODIFIER||1375|c.-1375C>A|499|ansP|protein_coding|CODING|b1453||AGT),upstream_gene_variant(MODIFIER||1376|c.-1376_-1375insC|499|ansP|protein_coding|CODING|b1453||AGGG),upstream_gene_variant(MODIFIER||547|c.-547G>T|678|rhsE|protein_coding|CODING|b1456||AGT|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||546|c.-547_-546insG|678|rhsE|protein_coding|CODING|b1456||AGGG|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||2567|c.-2567G>T|160|ydcD|protein_coding|CODING|b1457||AGT),upstream_gene_variant(MODIFIER||2566|c.-2567_-2566insG|160|ydcD|protein_coding|CODING|b1457||AGGG),upstream_gene_variant(MODIFIER||3231|c.-3231G>T|350|yncI|protein_coding|CODING|b1459||AGT|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||3230|c.-3231_-3230insG|350|yncI|protein_coding|CODING|b1459||AGGG|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||4461|c.-4461G>T|378|ydcC|protein_coding|CODING|b1460||AGT),upstream_gene_variant(MODIFIER||4460|c.-4461_-4460insG|378|ydcC|protein_coding|CODING|b1460||AGGG),downstream_gene_variant(MODIFIER||2987|c.*2987G>T|353|yncE|protein_coding|CODING|b1452||AGT),downstream_gene_variant(MODIFIER||2988|c.*2987_*2988insG|353|yncE|protein_coding|CODING|b1452||AGGG),downstream_gene_variant(MODIFIER||491|c.*491G>T|205|yncG|protein_coding|CODING|b1454||AGT),downstream_gene_variant(MODIFIER||492|c.*491_*492insG|205|yncG|protein_coding|CODING|b1454||AGGG),downstream_gene_variant(MODIFIER||203|c.*203G>T|70|yncH|protein_coding|CODING|b1455||AGT),downstream_gene_variant(MODIFIER||204|c.*203_*204insG|70|yncH|protein_coding|CODING|b1455||AGGG),intergenic_region(MODIFIER|||n.1525379G>T|||||||AGT),intergenic_region(MODIFIER|||n.1525379_1525380insG|||||||AGGG) GT:DP:AD:RO:QR:AO:QA:GL 0:19:19,0,0:19:734:0,0:0,0:0,-66.383,-66.383 0:10:6,2,2:6:242:2,2:71,77:0,-15.396,-14.852 0:83:83,0,0:83:3242:0,0:0,0:0,-291.874,-291.874
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
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74 U00096 1527079 . A G 7.60942E-10 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=2;CIGAR=1X;DP=67;DPB=67;DPRA=0.967742;EPP=7.35324;EPPR=8.65613;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=39.9846;NS=13;NUMALT=1;ODDS=22.6884;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=44;QR=2138;RO=65;RPL=2;RPP=7.35324;RPPR=7.05258;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=64;SRP=135.604;SRR=1;TYPE=snp;technology.ILLUMINA=1;EFF=missense_variant(MODERATE|MISSENSE|gAg/gGg|p.Glu385Gly/c.1154A>G|678|rhsE|protein_coding|CODING|b1456|1|G|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||3075|c.-3075T>C|499|ansP|protein_coding|CODING|b1453||G),upstream_gene_variant(MODIFIER||867|c.-867A>G|160|ydcD|protein_coding|CODING|b1457||G),upstream_gene_variant(MODIFIER||1531|c.-1531A>G|350|yncI|protein_coding|CODING|b1459||G|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||2761|c.-2761A>G|378|ydcC|protein_coding|CODING|b1460||G),upstream_gene_variant(MODIFIER||3997|c.-3997A>G|77|pptA|protein_coding|CODING|b1461||G),upstream_gene_variant(MODIFIER||4969|c.-4969A>G|281|nhoA|protein_coding|CODING|b1463||G),downstream_gene_variant(MODIFIER||4687|c.*4687A>G|353|yncE|protein_coding|CODING|b1452||G),downstream_gene_variant(MODIFIER||2191|c.*2191A>G|205|yncG|protein_coding|CODING|b1454||G),downstream_gene_variant(MODIFIER||1903|c.*1903A>G|70|yncH|protein_coding|CODING|b1455||G),downstream_gene_variant(MODIFIER||4227|c.*4227T>C|189|yddH|protein_coding|CODING|b1462||G) GT:DP:AD:RO:QR:AO:QA:GL 0:4:4,0:4:145:0:0:0,-12.7264 0:6:6,0:6:196:0:0:0,-17.3319 0:9:9,0:9:279:0:0:0,-24.5414
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
75 U00096 1527291 . G T 8.98077E-15 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=2;CIGAR=1X;DP=396;DPB=396;DPRA=0.215938;EPP=3.0103;EPPR=42.9311;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=13;NUMALT=1;ODDS=57.3966;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=13943;RO=393;RPL=0;RPP=7.35324;RPPR=39.2623;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=215;SRP=10.5745;SRR=178;TYPE=snp;technology.ILLUMINA=1;EFF=missense_variant(MODERATE|MISSENSE|Ggc/Tgc|p.Gly456Cys/c.1366G>T|678|rhsE|protein_coding|CODING|b1456|1|T|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||3287|c.-3287C>A|499|ansP|protein_coding|CODING|b1453||T),upstream_gene_variant(MODIFIER||655|c.-655G>T|160|ydcD|protein_coding|CODING|b1457||T),upstream_gene_variant(MODIFIER||1319|c.-1319G>T|350|yncI|protein_coding|CODING|b1459||T|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||2549|c.-2549G>T|378|ydcC|protein_coding|CODING|b1460||T),upstream_gene_variant(MODIFIER||3785|c.-3785G>T|77|pptA|protein_coding|CODING|b1461||T),upstream_gene_variant(MODIFIER||4757|c.-4757G>T|281|nhoA|protein_coding|CODING|b1463||T),downstream_gene_variant(MODIFIER||4899|c.*4899G>T|353|yncE|protein_coding|CODING|b1452||T),downstream_gene_variant(MODIFIER||2403|c.*2403G>T|205|yncG|protein_coding|CODING|b1454||T),downstream_gene_variant(MODIFIER||2115|c.*2115G>T|70|yncH|protein_coding|CODING|b1455||T),downstream_gene_variant(MODIFIER||4015|c.*4015C>A|189|yddH|protein_coding|CODING|b1462||T) GT:DP:AD:RO:QR:AO:QA:GL 0:12:12,0:12:422:0:0:0,-38.3029 0:12:12,0:12:418:0:0:0,-37.9417 0:48:48,0:48:1735:0:0:0,-156.391
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
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parents:
diff changeset
76 U00096 1527328 . A C 5.89448E-14 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=53;CIGAR=1X;DP=371;DPB=371;DPRA=0;EPP=53.2;EPPR=17.4595;GTI=0;LEN=1;MEANALT=1;MQM=59.7547;MQMR=59.9843;NS=13;NUMALT=1;ODDS=49.8508;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1375;QR=11600;RO=318;RPL=9;RPP=53.2;RPPR=3.44733;RPR=44;RUN=1;SAF=0;SAP=118.098;SAR=53;SRF=257;SRP=265.335;SRR=61;TYPE=snp;technology.ILLUMINA=1;EFF=missense_variant(MODERATE|MISSENSE|cAc/cCc|p.His468Pro/c.1403A>C|678|rhsE|protein_coding|CODING|b1456|1|C|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||3324|c.-3324T>G|499|ansP|protein_coding|CODING|b1453||C),upstream_gene_variant(MODIFIER||618|c.-618A>C|160|ydcD|protein_coding|CODING|b1457||C),upstream_gene_variant(MODIFIER||1282|c.-1282A>C|350|yncI|protein_coding|CODING|b1459||C|WARNING_TRANSCRIPT_NO_START_CODON),upstream_gene_variant(MODIFIER||2512|c.-2512A>C|378|ydcC|protein_coding|CODING|b1460||C),upstream_gene_variant(MODIFIER||3748|c.-3748A>C|77|pptA|protein_coding|CODING|b1461||C),upstream_gene_variant(MODIFIER||4720|c.-4720A>C|281|nhoA|protein_coding|CODING|b1463||C),downstream_gene_variant(MODIFIER||4936|c.*4936A>C|353|yncE|protein_coding|CODING|b1452||C),downstream_gene_variant(MODIFIER||2440|c.*2440A>C|205|yncG|protein_coding|CODING|b1454||C),downstream_gene_variant(MODIFIER||2152|c.*2152A>C|70|yncH|protein_coding|CODING|b1455||C),downstream_gene_variant(MODIFIER||3978|c.*3978T>G|189|yddH|protein_coding|CODING|b1462||C) GT:DP:AD:RO:QR:AO:QA:GL 0:22:17,5:17:627:5:112:0,-46.4475 0:11:10,1:10:378:1:22:0,-32.1693 0:33:31,2:31:1151:2:49:0,-99.2161
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
77 U00096 1532370 . G T 7.50367E-15 . AB=0;ABP=0;AC=0;AF=0;AN=12;AO=2;CIGAR=1X;DP=378;DPB=378;DPRA=0.268293;EPP=3.0103;EPPR=19.9408;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=12;NUMALT=1;ODDS=74.0204;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=13838;RO=374;RPL=2;RPP=7.35324;RPPR=5.82044;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=216;SRP=22.5419;SRR=158;TYPE=snp;technology.ILLUMINA=1;EFF=missense_variant(MODERATE|MISSENSE|cGt/cTt|p.Arg108Leu/c.323G>T|281|nhoA|protein_coding|CODING|b1463|1|T),upstream_gene_variant(MODIFIER||495|c.-495C>A|189|yddH|protein_coding|CODING|b1462||T),downstream_gene_variant(MODIFIER||4408|c.*4408G>T|678|rhsE|protein_coding|CODING|b1456||T|WARNING_TRANSCRIPT_NO_START_CODON),downstream_gene_variant(MODIFIER||3942|c.*3942G>T|160|ydcD|protein_coding|CODING|b1457||T),downstream_gene_variant(MODIFIER||2707|c.*2707G>T|350|yncI|protein_coding|CODING|b1459||T|WARNING_TRANSCRIPT_NO_START_CODON),downstream_gene_variant(MODIFIER||1394|c.*1394G>T|378|ydcC|protein_coding|CODING|b1460||T),downstream_gene_variant(MODIFIER||1061|c.*1061G>T|77|pptA|protein_coding|CODING|b1461||T),downstream_gene_variant(MODIFIER||619|c.*619C>A|297|yddE|protein_coding|CODING|b1464||T),downstream_gene_variant(MODIFIER||1591|c.*1591C>A|226|narV|protein_coding|CODING|b1465||T),downstream_gene_variant(MODIFIER||2268|c.*2268C>A|231|narW|protein_coding|CODING|b1466||T),downstream_gene_variant(MODIFIER||2963|c.*2963C>A|514|narY|protein_coding|CODING|b1467||T),downstream_gene_variant(MODIFIER||4504|c.*4504C>A|1246|narZ|protein_coding|CODING|b1468||T) GT:DP:AD:RO:QR:AO:QA:GL 0:16:16,0:16:583:0:0:0,-52.8004 0:9:7,2:7:249:2:76:0,-15.539 0:46:46,0:46:1675:0:0:0,-151.009
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents:
diff changeset
78 U00096 1533613 . T C 6.56972E-15 . AB=0;ABP=0;AC=0;AF=0;AN=13;AO=2;CIGAR=1X;DP=489;DPB=489;DPRA=0.0989691;EPP=3.0103;EPPR=70.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.9979;NS=13;NUMALT=1;ODDS=41.1942;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=18551;RO=487;RPL=0;RPP=7.35324;RPPR=96.7582;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=203;SRP=32.265;SRR=284;TYPE=snp;technology.ILLUMINA=1;EFF=synonymous_variant(LOW|SILENT|ggA/ggG|p.Gly90Gly/c.270A>G|297|yddE|protein_coding|CODING|b1464|1|C),upstream_gene_variant(MODIFIER||1738|c.-1738A>G|189|yddH|protein_coding|CODING|b1462||C),downstream_gene_variant(MODIFIER||3950|c.*3950T>C|350|yncI|protein_coding|CODING|b1459||C|WARNING_TRANSCRIPT_NO_START_CODON),downstream_gene_variant(MODIFIER||2637|c.*2637T>C|378|ydcC|protein_coding|CODING|b1460||C),downstream_gene_variant(MODIFIER||2304|c.*2304T>C|77|pptA|protein_coding|CODING|b1461||C),downstream_gene_variant(MODIFIER||720|c.*720T>C|281|nhoA|protein_coding|CODING|b1463||C),downstream_gene_variant(MODIFIER||348|c.*348A>G|226|narV|protein_coding|CODING|b1465||C),downstream_gene_variant(MODIFIER||1025|c.*1025A>G|231|narW|protein_coding|CODING|b1466||C),downstream_gene_variant(MODIFIER||1720|c.*1720A>G|514|narY|protein_coding|CODING|b1467||C),downstream_gene_variant(MODIFIER||3261|c.*3261A>G|1246|narZ|protein_coding|CODING|b1468||C) GT:DP:AD:RO:QR:AO:QA:GL 0:26:26,0:26:1013:0:0:0,-91.465 0:11:11,0:11:417:0:0:0,-37.8758 0:58:58,0:58:2210:0:0:0,-199.104