Unix and Linux Discussions Tagged with tab delimited file |
|
Thread / Thread Starter |
Last Post |
Replies |
Views |
Forum |
|
|
|
2 |
5,511 |
UNIX for Beginners Questions & Answers |
|
|
|
8 |
14,844 |
Programming |
|
|
|
1 |
4,834 |
Shell Programming and Scripting |
|
|
|
0 |
3,010 |
Shell Programming and Scripting |
|
|
|
1 |
6,498 |
Shell Programming and Scripting |
|
|
|
2 |
6,485 |
Shell Programming and Scripting |
|
|
|
3 |
5,268 |
Shell Programming and Scripting |
|
|
|
8 |
18,903 |
UNIX for Advanced & Expert Users |
|
|
|
8 |
10,327 |
Shell Programming and Scripting |
|
|
|
4 |
8,456 |
Shell Programming and Scripting |
|
|
|
9 |
12,305 |
Shell Programming and Scripting |
|
|
|
19 |
10,600 |
Shell Programming and Scripting |
|
|
|
16 |
69,967 |
UNIX for Dummies Questions & Answers |
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
vcf-isec 0.1.5 July 2011 VCF-ISEC(1)