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

AUTHORS¶

Erik Garrison and vcflib contributors.