VCFALLELICPRIMITIVES

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.