bio-vcf1

Usage

Overview

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