Man page - vcf-isec(1)

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Package: vcftools
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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