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1 '\" t
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2 .TH vcf 5 "August 2013" "htslib" "Bioinformatics formats"
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3 .SH NAME
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4 vcf \- Variant Call Format
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5 .\"
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6 .\" Copyright (C) 2011 Broad Institute.
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7 .\" Copyright (C) 2013 Genome Research Ltd.
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8 .\"
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9 .\" Author: Heng Li <lh3@sanger.ac.uk>
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10 .\"
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11 .\" Permission is hereby granted, free of charge, to any person obtaining a
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12 .\" copy of this software and associated documentation files (the "Software"),
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13 .\" to deal in the Software without restriction, including without limitation
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14 .\" the rights to use, copy, modify, merge, publish, distribute, sublicense,
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15 .\" and/or sell copies of the Software, and to permit persons to whom the
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16 .\" Software is furnished to do so, subject to the following conditions:
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17 .\"
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18 .\" The above copyright notice and this permission notice shall be included in
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19 .\" all copies or substantial portions of the Software.
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20 .\"
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21 .\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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22 .\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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23 .\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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24 .\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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25 .\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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26 .\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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27 .\" DEALINGS IN THE SOFTWARE.
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28 .\"
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29 .SH DESCRIPTION
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30 The Variant Call Format (VCF) is a TAB-delimited format with each data line
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31 consisting of the following fields:
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32 .TS
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33 nlbl.
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34 1 CHROM CHROMosome name
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35 2 POS the left-most POSition of the variant
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36 3 ID unique variant IDentifier
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37 4 REF the REFerence allele
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38 5 ALT the ALTernate allele(s) (comma-separated)
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39 6 QUAL variant/reference QUALity
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40 7 FILTER FILTERs applied
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41 8 INFO INFOrmation related to the variant (semicolon-separated)
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42 9 FORMAT FORMAT of the genotype fields (optional; colon-separated)
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43 10+ SAMPLE SAMPLE genotypes and per-sample information (optional)
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44 .TE
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45 .P
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46 The following table gives the \fBINFO\fP tags used by samtools and bcftools.
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47 .TP
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48 .B AF1
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49 Max-likelihood estimate of the site allele frequency (AF) of the first ALT allele
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50 (double)
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51 .TP
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52 .B DP
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53 Raw read depth (without quality filtering)
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54 (int)
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55 .TP
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56 .B DP4
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57 # high-quality reference forward bases, ref reverse, alternate for and alt rev bases
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58 (int[4])
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59 .TP
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60 .B FQ
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61 Consensus quality. Positive: sample genotypes different; negative: otherwise
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62 (int)
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63 .TP
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64 .B MQ
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65 Root-Mean-Square mapping quality of covering reads
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66 (int)
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67 .TP
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68 .B PC2
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69 Phred probability of AF in group1 samples being larger (,smaller) than in group2
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70 (int[2])
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71 .TP
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72 .B PCHI2
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73 Posterior weighted chi^2 P-value between group1 and group2 samples
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74 (double)
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75 .TP
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76 .B PV4
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77 P-value for strand bias, baseQ bias, mapQ bias and tail distance bias
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78 (double[4])
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79 .TP
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80 .B QCHI2
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81 Phred-scaled PCHI2
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82 (int)
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83 .TP
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84 .B RP
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85 # permutations yielding a smaller PCHI2
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86 (int)
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87 .TP
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88 .B CLR
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89 Phred log ratio of genotype likelihoods with and without the trio/pair constraint
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90 (int)
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91 .TP
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92 .B UGT
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93 Most probable genotype configuration without the trio constraint
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94 (string)
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95 .TP
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96 .B CGT
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97 Most probable configuration with the trio constraint
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98 (string)
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99 .TP
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100 .B VDB
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101 Tests variant positions within reads. Intended for filtering RNA-seq artifacts around splice sites
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102 (float)
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103 .TP
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104 .B RPB
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105 Mann-Whitney rank-sum test for tail distance bias
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106 (float)
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107 .TP
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108 .B HWE
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109 Hardy-Weinberg equilibrium test (Wigginton et al)
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110 (float)
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111 .P
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112 .SH SEE ALSO
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113 .TP
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114 https://github.com/samtools/hts-specs
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115 The full VCF/BCF file format specification
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116 .TP
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117 .I A note on exact tests of Hardy-Weinberg equilibrium
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118 Wigginton JE et al
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119 PMID:15789306
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120 .\" (http://www.ncbi.nlm.nih.gov/pubmed/15789306)
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