NAME

bio-vcf - domain specific language (DSL) for processing the VCF format

SYNOPSIS

bio-vcf [ options] filename

DESCRIPTION

bio-vcf 0.9.5 (biogem Ruby 2.7.2 with pcows) by Pjotr Prins 2015-2020
e.g. bio-vcf < test/data/input/somaticsniper.vcf
-i, --ignore-missing
Ignore missing data
--filter cmd
Evaluate filter on each record
--sfilter cmd
Evaluate filter on each sample
--sfilter-samples list
Filter on selected samples (e.g., 0,1
--ifilter, --if cmd
Include filter
--ifilter-samples list
Include set - implicitely defines exclude set
--efilter, --ef cmd
Exclude filter
--efilter-samples list
Exclude set - overrides exclude set
--add-filter name
Set/add filter field to name
--bed bedfile
Filter on BED elements
-e, --eval cmd
Evaluate command on each record
--eval-once cmd
Evaluate command once (usually for header info)
--seval cmd
Evaluate command on each sample
--rewrite eval
Rewrite INFO
--samples list
Output selected samples
--rdf
Generate Turtle RDF (also check out --template!)
--num-threads [num]
Multi-core version (default ALL)
--thread-lines num
Fork thread on num lines (default 40000)
--skip-header
Do not output VCF header info
--set-header list
Set a special tab delimited output header (#samples expands to sample names)
-t, --template erb
Use ERB template for output
--add-header-tag
Add bio-vcf status tag to header output
--timeout [num]
Timeout waiting for thread to complete (default 180)
--names
Output sample names
--statistics
Output statistics
-q, --quiet
Run quietly
-v, --verbose
Run verbosely
--debug
Show debug messages and keep intermediate output
--id name
Identifier
--tags list
Add tags
-h, --help
display this help and exit
Vcf parser

AUTHOR


This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.