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% VCFFILTER(1) vcffilter (vcflib) | vcffilter (VCF filter)
% Erik Garrison and vcflib contributors
# NAME
**vcffilter**
# SYNOPSIS
**vcffilter** [options] <vcf file>
# DESCRIPTION
VCF filter the specified vcf file using the set of filters.
# OPTIONS
<!--
>>> from rtest import run_stdout, head, cat, sh
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Current command line options:
```
>>> head("vcffilter -h",39)
vcflib filter the specified vcf file using the set of filters
>
usage: vcffilter [options] <vcf file>
>
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
# EXAMPLES
Filter VCF records that have an allele count > 10 results in 1471 matches for
```python
>>> sh("../build/vcffilter -f 'AC > 10' ../samples/grch38#chr4_10083863-10181258.vcf|wc -l")
546
```
# SEE ALSO
[vcflib](./vcflib.md)(1)
Note that [bio-vcf](https://github.com/vcflib/bio-vcf) may easily give 5x better performance. E.g.
```
bio-vcf --filter 'r.info.ac>10'
```
instead of
```
vcfffilter 'AC > 10'
```
will filter all AC fields larger than 10.
# OTHER
## Source code
[vcffilter.cpp](https://github.com/vcflib/vcflib/blob/master/src/vcffilter.cpp)
# LICENSE
Copyright 2011-2023 (C) Erik Garrison and vcflib contributors. MIT licensed.
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