Mercurial > repos > iuc > bcftools_convert_to_vcf

annotate test-data/convert.gvcf.vcf @ 19:4935320a59a8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 96c0663be587b73bdf09ddf060cb559f28f9eba7
author iuc
date Thu, 12 Jan 2023 15:48:05 +0000
parents b068ef999550
children
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b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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1 ##fileformat=VCFv4.1
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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2 ##FILTER=<ID=PASS,Description="All filters passed">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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3 ##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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4 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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5 ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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6 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Filtered basecall depth used for site genotyping">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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7 ##FORMAT=<ID=DPF,Number=1,Type=Integer,Description="Basecalls filtered from input prior to site genotyping">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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8 ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed. For indels this value only includes reads which confidently support each allele (posterior prob 0.999 or higher that read contains indicated allele vs all other intersecting indel alleles)">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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9 ##FORMAT=<ID=DPI,Number=1,Type=Integer,Description="Read depth associated with indel, taken from the site preceding the indel.">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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10 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the region described in this record">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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11 ##INFO=<ID=BLOCKAVG_min30p3a,Number=0,Type=Flag,Description="Non-variant site block. All sites in a block are constrained to be non-variant, have the same filter value, and have all sample values in range [x,y], y <= max(x+3,(x*1.3)). All printed site block sample values are the minimum observed in the region spanned by the block">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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12 ##INFO=<ID=SNVSB,Number=1,Type=Float,Description="SNV site strand bias">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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13 ##INFO=<ID=SNVHPOL,Number=1,Type=Integer,Description="SNV contextual homopolymer length">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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14 ##INFO=<ID=CIGAR,Number=A,Type=String,Description="CIGAR alignment for each alternate indel allele">
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15 ##INFO=<ID=RU,Number=A,Type=String,Description="Smallest repeating sequence unit extended or contracted in the indel allele relative to the reference. RUs are not reported if longer than 20 bases.">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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16 ##INFO=<ID=REFREP,Number=A,Type=Integer,Description="Number of times RU is repeated in reference.">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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17 ##INFO=<ID=IDREP,Number=A,Type=Integer,Description="Number of times RU is repeated in indel allele.">
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18 ##FILTER=<ID=IndelConflict,Description="Locus is in region with conflicting indel calls">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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19 ##FILTER=<ID=SiteConflict,Description="Site genotype conflicts with proximal indel call. This is typically a heterozygous SNV call made inside of a heterozygous deletion">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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20 ##FILTER=<ID=LowGQX,Description="Locus GQX is less than 30 or not present">
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21 ##FILTER=<ID=HighDPFRatio,Description="The fraction of basecalls filtered out at a site is greater than 0.3">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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22 ##FILTER=<ID=HighSNVSB,Description="SNV strand bias value (SNVSB) exceeds 10">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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23 ##FILTER=<ID=HighREFREP,Description="Locus contains an indel allele occurring in a homopolymer or dinucleotide track with a reference repeat greater than 8">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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24 ##FILTER=<ID=HighDepth,Description="Locus depth is greater than 3x the mean chromosome depth">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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25 ##contig=<ID=22,length=450>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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26 ##SnvTheta=0.001
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27 ##IndelTheta=0.0001
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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28 ##MaxDepth_1=114.18
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29 ##MaxDepth_10=131.73
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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30 ##MaxDepth_11=117.27
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31 ##MaxDepth_12=116.97
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32 ##MaxDepth_13=102.24
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33 ##MaxDepth_14=101.55
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34 ##MaxDepth_15=95.22
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35 ##MaxDepth_16=111.33
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36 ##MaxDepth_17=112.59
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37 ##MaxDepth_18=121.86
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38 ##MaxDepth_19=111.12
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39 ##MaxDepth_2=121.83
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40 ##MaxDepth_20=111.24
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41 ##MaxDepth_21=98.43
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42 ##MaxDepth_22=76.23
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43 ##MaxDepth_3=120.09
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44 ##MaxDepth_4=124.50
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45 ##MaxDepth_5=119.82
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46 ##MaxDepth_6=122.22
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47 ##MaxDepth_7=120.27
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48 ##MaxDepth_8=120.45
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49 ##MaxDepth_9=102.48
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50 ##MaxDepth_M=7005.66
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51 ##MaxDepth_X=61.05
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52 ##MaxDepth_Y=37.17
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53 ##FILTER=<ID=IndelSizeFilter,Description="Indel is outside reportable size range. Insertion range: [1,3], Deletion range: [1,11]">
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54 ##gvcftools_version="0.16"
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55 ##FILTER=<ID=HAPLOID_CONFLICT,Description="Locus has heterozygous genotype in a haploid region.">
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56 ##FORMAT=<ID=OPL,Number=.,Type=Integer,Description="Original PL value before ploidy correction">
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57 ##INFO=<ID=phastCons,Number=0,Type=Flag,Description="overlaps a phastCons element">
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58 ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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59 ##INFO=<ID=AF,Number=A,Type=String,Description="1000 Genomes Allele Frequency based on AC/AN; Format: Allele:AlleleFrequency">
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60 ##INFO=<ID=AMR_AF,Number=A,Type=String,Description="1000 Genomes Allele Frequency for samples from AMR population based on AC/AN; Format: Allele:AlleleFrequency">
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61 ##INFO=<ID=ASN_AF,Number=A,Type=String,Description="1000 Genomes Allele Frequency for samples from ASN population based on AC/AN; Format: Allele:AlleleFrequency">
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62 ##INFO=<ID=AFR_AF,Number=A,Type=String,Description="1000 Genomes Allele Frequency for samples from AFR population based on AC/AN; Format: Allele:AlleleFrequency">
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63 ##INFO=<ID=EUR_AF,Number=A,Type=String,Description="1000 Genomes Allele Frequency for samples from EUR population based on AC/AN; Format: Allele:AlleleFrequency">
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64 ##INFO=<ID=CLNACC,Number=.,Type=String,Description="Accession and version number assigned by ClinVar to the genotype/phenotype relationship. Multiple entries for an allele are pipe-delimited">
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65 ##INFO=<ID=CLNSIG,Number=.,Type=String,Description="String that describes the clinical significance. Possible values: unknown, untested, non-pathogenic, probable-non-pathogenic, probable-pathogenic, pathogenic, drug-response, histocompatibility, other. Multiple values are pipe-delimited">
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66 ##INFO=<ID=CLNORIGIN,Number=.,Type=String,Description="String that describes the origin of the variant allele. Possible values: unknown, germline, somatic, inherited, paternal, maternal, de-novo, biparental, uniparental, not-tested, test-inconclusive, other. Multiple values for an allele are pipe-delimited">
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67 ##INFO=<ID=CLNSRC,Number=.,Type=String,Description="Variant clinical source or channel. Multiple values for an allele are pipe-delimited">
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68 ##INFO=<ID=CLNSRCID,Number=.,Type=String,Description="Identifier used by source defined in CLNSRC. Multiple values are pipe-delimited">
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69 ##INFO=<ID=CLNGENEINFO,Number=.,Type=String,Description="Gene symbol(s) and NCBI GeneID(s). The gene symbol and ID are delimited by a colon and multiple such pairs are pipe-delimited, Example SYMBOL1:GeneID1|SYMBOL2:GeneID2">
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70 ##INFO=<ID=CLNDBN,Number=.,Type=String,Description="Disease name used by the database specified by CLNSRC. Values corresponding to each CLNACC entry are pipe-delimited">
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71 ##INFO=<ID=CLNDSDB,Number=.,Type=String,Description="Colon-delimited list of variant disease database name(s). Multiple values from a single database are pipe-delimited">
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72 ##INFO=<ID=CLNDSDBID,Number=.,Type=String,Description="Colon-delimited list of variant disease database identifier(s). Multiple values from a single database are pipe-delimited">
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73 ##INFO=<ID=CSQ,Number=A,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|EXON|INTRON|HGNC|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|CANONICAL|SIFT|PolyPhen|GMAF|ENSP|DOMAINS|CCDS|HGVSc|HGVSp|CELL_TYPE">
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74 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE99
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75 22 1 . N . 0 LowGQX END=9;BLOCKAVG_min30p3a GT:GQX:DP:DPF .:.:0:0
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76 22 10 . C . 0 LowGQX END=20;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:5:2:0
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