Mercurial > repos > jjohnson > bcftools_plugin_impute_info

annotate test-data/convert.gvcf.vcf @ 1:f125988aa89e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sun, 26 Jun 2016 15:40:03 -0400
parents 8dcc53e60847
children
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8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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1 ##fileformat=VCFv4.1
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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2 ##FILTER=<ID=PASS,Description="All filters passed">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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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}">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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4 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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5 ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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6 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Filtered basecall depth used for site genotyping">
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7 ##FORMAT=<ID=DPF,Number=1,Type=Integer,Description="Basecalls filtered from input prior to site genotyping">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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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)">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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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.">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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10 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the region described in this record">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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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">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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12 ##INFO=<ID=SNVSB,Number=1,Type=Float,Description="SNV site strand bias">
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13 ##INFO=<ID=SNVHPOL,Number=1,Type=Integer,Description="SNV contextual homopolymer length">
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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.">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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16 ##INFO=<ID=REFREP,Number=A,Type=Integer,Description="Number of times RU is repeated in reference.">
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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">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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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">
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20 ##FILTER=<ID=LowGQX,Description="Locus GQX is less than 30 or not present">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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21 ##FILTER=<ID=HighDPFRatio,Description="The fraction of basecalls filtered out at a site is greater than 0.3">
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22 ##FILTER=<ID=HighSNVSB,Description="SNV strand bias value (SNVSB) exceeds 10">
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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">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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24 ##FILTER=<ID=HighDepth,Description="Locus depth is greater than 3x the mean chromosome depth">
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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25 ##contig=<ID=22,length=450>
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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26 ##SnvTheta=0.001
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27 ##IndelTheta=0.0001
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28 ##MaxDepth_1=114.18
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29 ##MaxDepth_10=131.73
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30 ##MaxDepth_11=117.27
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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31 ##MaxDepth_12=116.97
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32 ##MaxDepth_13=102.24
8dcc53e60847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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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">
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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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83 22 86 . G C 23 LowGQX SNVSB=0;SNVHPOL=2 GT:GQ:GQX:DP:DPF:AD 0/1:56:23:22:0:16,6
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