.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH BIO-VCF "1" "September 2021" "bio-vcf 0.9.5" "User Commands"
.SH NAME
bio-vcf \- domain specific language (DSL) for processing the VCF format
.SH SYNOPSIS
.B bio-vcf
[\fI\,options\/\fR] \fI\,filename\/\fR
.SH DESCRIPTION
bio\-vcf 0.9.5 (biogem Ruby 2.7.2 with pcows) by Pjotr Prins 2015\-2020
.PP
e.g.  bio\-vcf < test/data/input/somaticsniper.vcf
.TP
\fB\-i\fR, \fB\-\-ignore\-missing\fR
Ignore missing data
.TP
\fB\-\-filter\fR cmd
Evaluate filter on each record
.TP
\fB\-\-sfilter\fR cmd
Evaluate filter on each sample
.TP
\fB\-\-sfilter\-samples\fR list
Filter on selected samples (e.g., 0,1
.TP
\fB\-\-ifilter\fR, \fB\-\-if\fR cmd
Include filter
.TP
\fB\-\-ifilter\-samples\fR list
Include set \- implicitely defines exclude set
.TP
\fB\-\-efilter\fR, \fB\-\-ef\fR cmd
Exclude filter
.TP
\fB\-\-efilter\-samples\fR list
Exclude set \- overrides exclude set
.TP
\fB\-\-add\-filter\fR name
Set/add filter field to name
.TP
\fB\-\-bed\fR bedfile
Filter on BED elements
.TP
\fB\-e\fR, \fB\-\-eval\fR cmd
Evaluate command on each record
.TP
\fB\-\-eval\-once\fR cmd
Evaluate command once (usually for header info)
.TP
\fB\-\-seval\fR cmd
Evaluate command on each sample
.TP
\fB\-\-rewrite\fR eval
Rewrite INFO
.TP
\fB\-\-samples\fR list
Output selected samples
.TP
\fB\-\-rdf\fR
Generate Turtle RDF (also check out \fB\-\-template\fR!)
.TP
\fB\-\-num\-threads\fR [num]
Multi\-core version (default ALL)
.TP
\fB\-\-thread\-lines\fR num
Fork thread on num lines (default 40000)
.TP
\fB\-\-skip\-header\fR
Do not output VCF header info
.TP
\fB\-\-set\-header\fR list
Set a special tab delimited output header (#samples expands to sample names)
.TP
\fB\-t\fR, \fB\-\-template\fR erb
Use ERB template for output
.TP
\fB\-\-add\-header\-tag\fR
Add bio\-vcf status tag to header output
.TP
\fB\-\-timeout\fR [num]
Timeout waiting for thread to complete (default 180)
.TP
\fB\-\-names\fR
Output sample names
.TP
\fB\-\-statistics\fR
Output statistics
.TP
\fB\-q\fR, \fB\-\-quiet\fR
Run quietly
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Run verbosely
.TP
\fB\-\-debug\fR
Show debug messages and keep intermediate output
.TP
\fB\-\-id\fR name
Identifier
.TP
\fB\-\-tags\fR list
Add tags
.TP
\fB\-h\fR, \fB\-\-help\fR
display this help and exit
.PP
Vcf parser
.SH AUTHOR
 This manpage was written by Nilesh Patra for the Debian distribution and
 can be used for any other usage of the program.