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% VCFINTERSECT(1) vcfintersect (vcflib) | vcfintersect (VCF transformation)
% Erik Garrison and vcflib contributors
# NAME
**vcfintersect**
# SYNOPSIS
**vcfintersect** [options] [<vcf file>]
# DESCRIPTION
VCF set analysis
# OPTIONS
```
options:
-b, --bed FILE use intervals provided by this BED file
-R, --region REGION use 1-based tabix-style region (e.g. chrZ:10-20), multiples allowed
-S, --start-only don't use the reference length information in the record to determine
overlap status, just use the start posiion
-v, --invert invert the selection, printing only records which would
not have been printed out
-i, --intersect-vcf FILE use this VCF for set intersection generation
-u, --union-vcf FILE use this VCF for set union generation
-w, --window-size N compare records up to this many bp away (default 30)
-r, --reference FILE FASTA reference file, required with -i and -u
-l, --loci output whole loci when one alternate allele matches
-m, --ref-match intersect on the basis of record REF string
-t, --tag TAG attach TAG to each record's info field if it would intersect
-V, --tag-value VAL use this value to indicate that the allele is passing
'.' will be used otherwise. default: 'PASS'
-M, --merge-from FROM-TAG
-T, --merge-to TO-TAG merge from FROM-TAG used in the -i file, setting TO-TAG
in the current file.
For bed-vcf intersection, alleles which fall into the targets are retained.
Haplotype aware intersection, union and complement. Use for intersection and union of VCF files: unify on equivalent alleles within window-size bp
as determined by haplotype comparison alleles.
type: transformation
```
# EXIT VALUES
**0**
: Success
**not 0**
: Failure
# SEE ALSO
[vcflib](./vcflib.md)(1)
# OTHER
## Source code
[vcfintersect.cpp](https://github.com/vcflib/vcflib/blob/master/src/vcfintersect.cpp)
# LICENSE
Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed.
Copyright 2020-2024 (C) Pjotr Prins.
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