.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.4.
.TH VCF-ISEC "1" "July 2011" "vcf-isec 0.1.5" "User Commands"
.SH NAME
vcf-isec \- create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files
.SH SYNOPSIS
.B vcf-isec
[\fIOPTIONS\fR] \fIfile1.vcf file2.vcf \fR...
.SH DESCRIPTION
About: Create intersections, unions, complements on bgzipped and tabix indexed VCF or tab\-delimited files.
.IP
Note that lines from all files can be intermixed together on the output, which can yield
unexpected results.
.SH OPTIONS
.TP
\fB\-C\fR, \fB\-\-chromosomes\fR <list|file>
Process the given chromosomes (comma\-separated list or one chromosome per line in a file).
.TP
\fB\-c\fR, \fB\-\-complement\fR
Output positions present in the first file but missing from the other files.
.TP
\fB\-d\fR, \fB\-\-debug\fR
Debugging information
.TP
\fB\-f\fR, \fB\-\-force\fR
Continue even if the script complains about differing columns.
.TP
\fB\-o\fR, \fB\-\-one\-file\-only\fR
Print only entries from the left\-most file. Without \fB\-o\fR, all unique positions will be printed.
.TP
\fB\-n\fR, \fB\-\-nfiles\fR [+\-=]<int>
Output positions present in this many (=), this many or more (+), or this many or fewer (\-) files.
.TP
\fB\-p\fR, \fB\-\-prefix\fR <path>
If present, multiple files will be created with all possible isec combinations. (Suitable for Venn Diagram analysis.)
.TP
\fB\-t\fR, \fB\-\-tab\fR <chr:pos:file>
Tab\-delimited file with indexes of chromosome and position columns. (1\-based indexes)
.TP
\fB\-w\fR, \fB\-\-win\fR <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).
.TP
\fB\-h\fR, \-?, \fB\-\-help\fR
This help message.
.SH EXAMPLES
.IP
bgzip file.vcf; tabix \fB\-p\fR vcf file.vcf.gz
bgzip file.tab; tabix \fB\-s\fR 1 \fB\-b\fR 2 \fB\-e\fR 2 file.tab.gz