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

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. Default: filename = NULL.

Value

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

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

Author

Thierry Gosselin thierrygosselin@icloud.com