1% VCFFILTER(1) vcffilter (vcflib) | vcffilter (VCF filter)
2% Erik Garrison and vcflib contributors
3
4# NAME
5
6**vcffilter**
7
8# SYNOPSIS
9
10**vcffilter** [options] <vcf file>
11
12# DESCRIPTION
13
14VCF filter the specified vcf file using the set of filters
15
16
17
18# OPTIONS
19
20```
21
22
23options:
24    -f, --info-filter     specifies a filter to apply to the info fields of records,
25                          removes alleles which do not pass the filter
26    -g, --genotype-filter specifies a filter to apply to the genotype fields of records
27    -k, --keep-info       used in conjunction with '-g', keeps variant info, but removes genotype
28    -s, --filter-sites    filter entire records, not just alleles
29    -t, --tag-pass        tag vcf records as positively filtered with this tag, print all records
30    -F, --tag-fail        tag vcf records as negatively filtered with this tag, print all records
31    -A, --append-filter   append the existing filter tag, don't just replace it
32    -a, --allele-tag      apply -t on a per-allele basis.  adds or sets the corresponding INFO field tag
33    -v, --invert          inverts the filter, e.g. grep -v
34    -o, --or              use logical OR instead of AND to combine filters
35    -r, --region          specify a region on which to target the filtering, requires a BGZF
36                          compressed file which has been indexed with tabix.  any number of
37                          regions may be specified.
38
39Filter the specified vcf file using the set of filters.
40Filters are specified in the form "<ID> <operator> <value>:
41 -f "DP > 10"  # for info fields
42 -g "GT = 1|1" # for genotype fields
43 -f "CpG"  # for 'flag' fields
44
45Operators can be any of: =, !, <, >, |, &
46
47Any number of filters may be specified.  They are combined via logical AND
48unless --or is specified on the command line.  Obtain logical negation through
49the use of parentheses, e.g. "! ( DP = 10 )"
50
51For convenience, you can specify "QUAL" to refer to the quality of the site, even
52though it does not appear in the INFO fields.
53
54type: filter
55
56```
57
58
59
60
61
62# EXIT VALUES
63
64**0**
65: Success
66
67**not 0**
68: Failure
69
70# SEE ALSO
71
72
73
74[vcflib](./vcflib.md)(1)
75
76
77
78# OTHER
79
80## Source code
81
82[vcffilter.cpp](https://github.com/vcflib/vcflib/blob/master/src/vcffilter.cpp)
83
84# LICENSE
85
86Copyright 2011-2020 (C) Erik Garrison and vcflib contributors. MIT licensed.
87
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