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.TH "VCFINTERSECT" "1" "" "vcfintersect (vcflib)" "vcfintersect (VCF
transformation)"
.hy
.SH NAME
.PP
\f[B]vcfintersect\f[R]
.SH SYNOPSIS
.PP
\f[B]vcfintersect\f[R] options []
.SH DESCRIPTION
.PP
VCF set analysis
.SH OPTIONS
.IP
.nf
\f[C]


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\[aq]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\[aq]s info field if it would intersect
    -V, --tag-value VAL       use this value to indicate that the allele is passing
                              \[aq].\[aq] will be used otherwise.  default: \[aq]PASS\[aq]
    -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
\f[R]
.fi
.SH EXIT VALUES
.TP
.B \f[B]0\f[R]
Success
.TP
.B \f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2020 (C) Erik Garrison and vcflib contributors.
MIT licensed.
.SH AUTHORS
Erik Garrison and vcflib contributors.