NAME

vcffilter

SYNOPSIS

vcffilter options

DESCRIPTION

VCF filter the specified vcf file using the set of filters

OPTIONS

options:


    -f, --info-filter     specifies a filter to apply to the info fields of records,


                          removes alleles which do not pass the filter


    -g, --genotype-filter specifies a filter to apply to the genotype fields of records


    -k, --keep-info       used in conjunction with '-g', keeps variant info, but removes genotype


    -s, --filter-sites    filter entire records, not just alleles


    -t, --tag-pass        tag vcf records as positively filtered with this tag, print all records


    -F, --tag-fail        tag vcf records as negatively filtered with this tag, print all records


    -A, --append-filter   append the existing filter tag, don't just replace it


    -a, --allele-tag      apply -t on a per-allele basis.  adds or sets the corresponding INFO field tag


    -v, --invert          inverts the filter, e.g. grep -v


    -o, --or              use logical OR instead of AND to combine filters


    -r, --region          specify a region on which to target the filtering, requires a BGZF


                          compressed file which has been indexed with tabix.  any number of


                          regions may be specified.
Filter the specified vcf file using the set of filters.
Filters are specified in the form "<ID> <operator> <value>:


 -f "DP > 10"  # for info fields


 -g "GT = 1|1" # for genotype fields


 -f "CpG"  # for 'flag' fields
Operators can be any of: =, !, <, >, |, &
Any number of filters may be specified.  They are combined via logical AND
unless --or is specified on the command line.  Obtain logical negation through
the use of parentheses, e.g. "! ( DP = 10 )"
For convenience, you can specify "QUAL" to refer to the quality of the site, even
though it does not appear in the INFO fields.
type: filter
    

EXIT VALUES

0

Success

not 0

Failure

SEE ALSO

vcflib(1)

OTHER

LICENSE

Copyright 2011-2025 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2025 (C) Pjotr Prins.

AUTHORS

Erik Garrison and vcflib contributors.