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