table of contents
VCF-ISEC(1) | User Commands | VCF-ISEC(1) |
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
July 2011 | vcf-isec 0.1.5 |