markValidity: Check Validity of VCF for Ploidyverse Applications

In ploidyverse/ploidyverseClasses: Accessors and Utilities for VCFs in the Ploidyverse

Description

markValidity checks a VCF object to determine whether it if properly formatted for genotype calling using ploidyverse software, whether gentoypes have already been called using ploidyverse software, and whether the VCF meets ploidyverse standards for data archiving. A section is added to the VCF header to indicate the results of this check.

validPloidyverseVCF_Precall, validPloidyverseVCF_Postcall, and validPloidyverseVCF_Archival examine the header information generated by markValidity to return TRUE or FALSE.

Together, these functions can be used for error checking before calling genotypes or performing downstream analysis. markValidity also provides useful, human-readable information when the VCF object is written back to a file.

Usage

markValidity(object)

validPloidyverseVCF_Precall(object)
validPloidyverseVCF_Postcall(object)
validPloidyverseVCF_Archival(object)

Arguments

object

A VCF object.

Details

For a VCF to be valid for "Precall", "Postcall", or "Archival", it must contain the "AD" genotype field indicating allelic read depth.

For a VCF to be valid for "Postcall", it must contain the "GP" genotype field indicating genotype posterior probabilities.

For a VCF to be valid for "Archival", it must contain tag sequences in the INFO column if a non-reference pipeline was used, or contig lengths and assembly names if a reference pipeline was used. It must also contain a "SAMPLE" header line indicating the species and ploidy of every sample in the file.

Value

markValidity returns a VCF object, with a DataFrame called ploidyverseValidity added to meta(header(object)). There are three rows, named "ploidyversePrecall", "ploidyversePostcall", and "ploidyverseArchival". A column named "Valid" contains 1 if the VCF object passed the corresponding checks, and 0 if it didn't. A column named "Description" contains human-readable descriptions of the results of each check.

validPloidyverseVCF_Precall, validPloidyverseVCF_Postcall, and validPloidyverseVCF_Archival return TRUE if the corresponding value in the "Valid" column is 1, and FALSE otherwise.

Author(s)

Lindsay V. Clark

See Also

sampleinfo

Examples

# To be added

ploidyverse/ploidyverseClasses documentation built on May 25, 2019, 2:21 p.m.