bed2vcf

Genomic regions processing using open-source command line tools such as 'BEDTools', 'BEDOPS' and 'Tabix'.
These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging.
bedr API enhances access to these tools as well as offers additional utilities for genomic regions processing.

Paul C. Boutros

bedr

Genomic Region Processing using Tools Such as 'BEDTools',
'BEDOPS' and 'Tabix'

Syed Haider

Daryl Waggott

Emilie Lalonde

Clement Fung

Helena Winata

Dan Knight

Michael Chirico

Melinda Luo

bed2vcf function

<dl> <dt>x</dt>
<dd>the input bed object</dd> <dt>filename</dt>
<dd>a filename to write to.</dd> <dt>zero.based</dt>
<dd>is the file zero based i.e. bed format. defaults to true.</dd> <dt>header</dt>
<dd>a list of things to put in the header. repeated elements such as INFO, FILTER, FORMAT can be put in data.frames.</dd> <dt>fasta</dt>
<dd>build of the genome in fasta format</dd></dl>

Arguments

Author

convert bed to vcf — bed2vcf

<dl>

 <dt>x</dt>
<dd>the input bed object</dd>

 <dt>filename</dt>
<dd>a filename to write to.</dd>

 <dt>zero.based</dt>
<dd>is the file zero based i.e. bed format. defaults to true.</dd>

 <dt>header</dt>
<dd>a list of things to put in the header. repeated elements such as INFO, FILTER, FORMAT can be put in data.frames.</dd>

 <dt>fasta</dt>
<dd>build of the genome in fasta format</dd>

</dl>

convert bed to vcf

bed2vcf: convert bed to vcf

Description

Usage

Arguments

Author

Examples