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.TH "VCFANNOTATE" "1" "" "vcfannotate (vcflib)" "vcfannotate (VCF transformation)"
.hy
.SH NAME
.PP
\f[B]vcfannotate\f[R]
.SH SYNOPSIS
.PP
\f[B]vcfannotate\f[R] options []
.SH DESCRIPTION
.PP
Intersect the records in the VCF file with targets provided in a BED
file.
Intersections are done on the reference sequences in the VCF file.
If no VCF filename is specified on the command line (last argument) the
VCF read from stdin.
.SH OPTIONS
.IP
.nf
\f[C]


options:
    -b, --bed   use annotations provided by this BED file
    -k, --key   use this INFO field key for the annotations
    -d, --default  use this INFO field key for records without annotations

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.