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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
.TH VCF-COMPARE "1" "July 2011" "vcf-compare 0.1.5" "User Commands"
.SH NAME
vcf-compare \- compare bgzipped and tabix indexed VCF files
.SH SYNOPSIS
.B compare-vcf
[\fIOPTIONS\fR] \fIfile1.vcf file2.vcf \fR...
.SH DESCRIPTION
About: Compare bgzipped and tabix indexed VCF files. (E.g. bgzip file.vcf; tabix \fB\-p\fR vcf file.vcf.gz)
.SH OPTIONS
.TP
\fB\-c\fR, \fB\-\-chromosomes\fR <list|file>
Same as \fB\-r\fR, left for backward compatibility. Please do not use as it will be dropped in the future.
.TP
\fB\-d\fR, \fB\-\-debug\fR
Debugging information. Giving the option multiple times increases verbosity
.TP
\fB\-H\fR, \fB\-\-cmp\-haplotypes\fR
Compare haplotypes, not only positions
.TP
\fB\-m\fR, \fB\-\-name\-mapping\fR <list|file>
Use with \fB\-H\fR when comparing files with differing column names. The argument to this options is a
comma\-separated list or one mapping per line in a file. The names are colon separated and must
appear in the same order as the files on the command line.
.TP
\fB\-R\fR, \fB\-\-refseq\fR <file>
Compare the actual sequence, not just positions. Use with \fB\-w\fR to compare indels.
.TP
\fB\-r\fR, \fB\-\-regions\fR <list|file>
Process the given regions (comma\-separated list or one region per line in a file).
.TP
\fB\-s\fR, \fB\-\-samples\fR <list>
Process only the listed samples. Excluding unwanted samples may increase performance considerably.
.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.
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