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