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.