---
name: "bio-vcf"
section: "1"
platform: "linux"
package: "bio-vcf"
version: "0.9.5-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bio-vcf"
---

# bio-vcf(1)

domain specific language (DSL) for processing the VCF format

## 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.