vcf_strata: Join stratification metadata to a VCF (population-aware VCF)

In thierrygosselin/radiator: RADseq Data Exploration, Manipulation and Visualization using R

Join stratification metadata to a VCF (population-aware VCF)

Description

Include stratification metadata, e.g. population-level information, to the FORMAT field of a VCF file.

Usage

vcf_strata(data, strata, filename = NULL)

Arguments

data	A VCF file
strata	(optional) A tab delimited file at least 2 columns with header: INDIVIDUALS and STRATA. The STRATA and any other columns can be any hierarchical grouping. To create a strata file see individuals2strata.
filename	(optional) The file name for the modifed VCF, written to the working directory. Default: filename = NULL will make a custom filename with data and time.

Value

A VCF file in the working directory with new FORMAT field(s) correponding to the strata column(s).

Author(s)

Thierry Gosselin [e-mail]

References

Danecek P, Auton A, Abecasis G et al. (2011) The variant call format and VCFtools. Bioinformatics, 27, 2156-2158.

See Also

VCF web page

https://vcftools.github.io/specs.html

thierrygosselin/radiator documentation built on May 5, 2024, 5:12 a.m.