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.TH "VCFALLELICPRIMITIVES" "1" "" "vcfallelicprimitives (vcflib)" "vcfallelicprimitives (VCF transformation)"
.hy
.SH NAME
.PP
\f[B]vcfallelicprimitives\f[R]
.SH SYNOPSIS
.PP
\f[B]vcfallelicprimitives\f[R] options [file]
.SH DESCRIPTION
.PP
If multiple allelic primitives (gaps or mismatches) are specified in a
single VCF record, split the record into multiple lines, but drop all
INFO fields.
Does not handle genotypes (yet).
MNPs are split into multiple SNPs unless the -m flag is provided.
Records generated by splits have th
.SH OPTIONS
.IP
.nf
\f[C]

options:
    -m, --use-mnps          Retain MNPs as separate events (default: false).
    -t, --tag-parsed FLAG   Tag records which are split apart of a complex allele with this flag.
    -L, --max-length LEN    Do not manipulate records in which either the ALT or
                            REF is longer than LEN (default: 200).
    -k, --keep-info         Maintain site and allele-level annotations when decomposing.
                            Note that in many cases, such as multisample VCFs, these won\[aq]t
                            be valid post-decomposition.  For biallelic loci in single-sample
                            VCFs, they should be usable with caution.
    -g, --keep-geno         Maintain genotype-level annotations when decomposing.  Similar
                            caution should be used for this as for --keep-info.

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.