Provided by: vcftools_0.1.16-1_amd64
vcf-isec - create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files
vcf-isec [OPTIONS] file1.vcf file2.vcf ...
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.
-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.
bgzip file.vcf; tabix -p vcf file.vcf.gz bgzip file.tab; tabix -s 1 -b 2 -e 2 file.tab.gz