NAME

       vcf-isec  - create intersections, unions, complements on bgzipped and tabix indexed VCF or
       tab-delimited files

SYNOPSIS

       vcf-isec [OPTIONS] file1.vcf file2.vcf ...

DESCRIPTION

       About: Create intersections, unions, complements on bgzipped  and  tabix  indexed  VCF  or
       tab-delimited files.

              Note  that lines from all files can be intermixed together on the output, which can
              yield unexpected results.

OPTIONS

       -C, --chromosomes <list|file>
              Process the given chromosomes (comma-separated list or one chromosome per line in a
              file).

       -c, --complement
              Output positions present in the first file but missing from the other files.

       -d, --debug
              Debugging information

       -f, --force
              Continue even if the script complains about differing columns.

       -o, --one-file-only
              Print  only  entries from the left-most file. Without -o, all unique positions will
              be printed.

       -n, --nfiles [+-=]<int>
              Output positions present in this many (=), this many or more (+), or this  many  or
              fewer (-) files.

       -p, --prefix <path>
              If  present,  multiple  files  will be created with all possible isec combinations.
              (Suitable for Venn Diagram analysis.)

       -t, --tab <chr:pos:file>
              Tab-delimited file with  indexes  of  chromosome  and  position  columns.  (1-based
              indexes)

       -w, --win <int>
              In  repetitive  sequences,  the  same  indel  can be called at different positions.
              Consider records this far apart as matching (be it a SNP or an indel).

       -h, -?, --help
              This help message.

EXAMPLES

              bgzip file.vcf; tabix -p vcf file.vcf.gz bgzip file.tab; tabix  -s  1  -b  2  -e  2
              file.tab.gz