.\" 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 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 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 Compare the actual sequence, not just positions. Use with \fB\-w\fR to compare indels. .TP \fB\-r\fR, \fB\-\-regions\fR Process the given regions (comma\-separated list or one region per line in a file). .TP \fB\-s\fR, \fB\-\-samples\fR Process only the listed samples. Excluding unwanted samples may increase performance considerably. .TP \fB\-w\fR, \fB\-\-win\fR 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.