NAME

       vcfallelicprimitives

SYNOPSIS

       vcfallelicprimitives options [file]

DESCRIPTION

       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

OPTIONS

              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'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

EXIT VALUES

       0      Success

       not 0  Failure

SEE ALSO

       vcflib(1)

OTHER

LICENSE

       Copyright 2011-2022 (C) Erik Garrison and vcflib contributors.  MIT licensed.

AUTHORS

       Erik Garrison and vcflib contributors.