This is the command vcf-isec that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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