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