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.