Skip to contents

Save genotypes from the tree sequence as a VCF file

Source: R/tree-sequences.R
ts_vcf.Rd

This function writes a VCF file with diploid genotypes from a given tree sequence.

Usage

ts_vcf(
  ts,
  path,
  chrom = "chr1",
  individuals = NULL,
  position_transform = "lambda x: np.fmax(1, x)"
)

Arguments

ts

Tree sequence object of the class slendr_ts

path

Path to a VCF file

chrom

Chromosome name to be written in the CHROM column of the VCF (default value will be "chr1").

individuals

A vector of individuals in the tree sequence to extract genotypes from. If missing, all individuals present in the tree sequence will be saved. For a slendr-based tree sequence a character vector of individual names is expected. For non-slendr tree sequences, a numeric vector of IDs of individuals is expected.

position_transform

How to transform coordinates in a tree sequence to coordinates in a VCF file? By default, any site with coordinate 0 is converted to a position 1 to ensure that the resulting VCF file adheres to the VCF specification. Setting this to NULL will disable this

Value

No return value, called for side effects

Details

Users should note that, as with many other tskit-based slendr functions, ts_vcf is intended to provide some convenient defaults. For instance, even for non-slendr tree sequences, it will name each individual in the genotype columns after their integer IDs. In other words, if the individuals function argument is given as c(1, 42, 123), the individuals will be named as "ind_1", "ind_42", and "ind_123", instead of "tsk_0", "tsk_1", and "tsk_2". That said, the reticulate-based Python interface of slendr allows calling the write_vcf function of tskit directly!

By default, simulating a tree sequence with msprime and exporting the genotypes into VCF can cause issues with some downstream software because the VCF specification does not allow sites with the position 0. By default ts_vcf automatically transforms a site with a zero coordinate to a coordinate 1. Setting position_transform to NULL will disable this, and tsv_vcf will save coordinates in their original form. See this discussion for more detail: https://github.com/tskit-dev/tskit/issues/2838#issuecomment-1931796988, as well as relevant topics in the tskit documentation on this issue, like here: https://tskit.dev/tskit/docs/latest/export.html#modifying-coordinates.