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 2011-2020 (C) Erik Garrison and vcflib contributors. MIT licensed.

AUTHORS¶

Erik Garrison and vcflib contributors.