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.\" Automatically generated by Pandoc 2.19.2
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.el \{\
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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
\f[B]0\f[R]
Success
.TP
\f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2024 (C) Erik Garrison and vcflib contributors.
MIT licensed.
Copyright 2020-2024 (C) Pjotr Prins.
.SH AUTHORS
Erik Garrison and vcflib contributors.
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