VCFINTERSECT(1)

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 2011-2023 (C) Erik Garrison and vcflib contributors. MIT licensed.

AUTHORS
Erik Garrison and vcflib contributors.