% VCFFILTER(1) vcffilter (vcflib) | vcffilter (VCF filter) % Erik Garrison and vcflib contributors
vcffilter
vcffilter [options]
VCF filter the specified vcf file using the set of filters
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
0 : Success
not 0 : Failure
vcflib(1)
Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.