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.\" Automatically generated by Pandoc 2.7.3
.\"
.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.
|
