gt_as_vcf

This function write a VCF from a <code>gen_tibble</code>.

We provide a tidy grammar of population genetics, facilitating
the manipulation and analysis of data on biallelic single nucleotide
polymorphisms (SNPs). 'tidypopgen' scales to very large genetic datasets
by storing genotypes on disk, and performing operations on them in
chunks, without ever loading all data in memory. The full
functionalities of the package are described in Carter et al. (2025)
<doi:10.1111/2041-210x.70204>.

Andrea Manica

tidypopgen

Tidy Population Genetics

Evie Carter

Eirlys Tysall

Chang Christopher

Shaun Purcell

Bengtsson Henrik

gt_as_vcf function

<dl><dt>x</dt>
<dd>a <code>gen_tibble</code>, with population coded as 'population'</dd>
<dt>file</dt>
<dd>the .vcf file name with a path, or NULL (the default) to use the
location of the backing files.</dd>
<dt>chunk_size</dt>
<dd>the number of loci processed at a time. Automatically set
if left to NULL</dd>
<dt>overwrite</dt>
<dd>logical, should the file be overwritten if it already
exists?</dd></dl>

Arguments

Convert a gen_tibble to a VCF — gt_as_vcf

<dl>

<dt>x</dt>
<dd>a <code>gen_tibble</code>, with population coded as 'population'</dd>


<dt>file</dt>
<dd>the .vcf file name with a path, or NULL (the default) to use the
location of the backing files.</dd>


<dt>chunk_size</dt>
<dd>the number of loci processed at a time. Automatically set
if left to NULL</dd>


<dt>overwrite</dt>
<dd>logical, should the file be overwritten if it already
exists?</dd>

</dl>

gt_as_vcf: Convert a `gen_tibble` to a VCF

Description

Usage

Value

Arguments

Examples