VCFINTERSECT

NAME

vcfintersect

SYNOPSIS

vcfintersect options []

DESCRIPTION

VCF set analysis

OPTIONS

options:
-b, --bed FILE use intervals provided by this BED file
-R, --region REGION use 1-based tabix-style region (e.g. chrZ:10-20), multiples allowed
-S, --start-only don't use the reference length information in the record to determine
overlap status, just use the start posiion
-v, --invert invert the selection, printing only records which would
not have been printed out
-i, --intersect-vcf FILE use this VCF for set intersection generation
-u, --union-vcf FILE use this VCF for set union generation
-w, --window-size N compare records up to this many bp away (default 30)
-r, --reference FILE FASTA reference file, required with -i and -u
-l, --loci output whole loci when one alternate allele matches
-m, --ref-match intersect on the basis of record REF string
-t, --tag TAG attach TAG to each record's info field if it would intersect
-V, --tag-value VAL use this value to indicate that the allele is passing
'.' will be used otherwise. default: 'PASS'
-M, --merge-from FROM-TAG
-T, --merge-to TO-TAG merge from FROM-TAG used in the -i file, setting TO-TAG
in the current file.

For bed-vcf intersection, alleles which fall into the targets are retained.

Haplotype aware intersection, union and complement. Use for intersection and union of VCF files: unify on equivalent alleles within window-size bp
as determined by haplotype comparison alleles.

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.