FixVcfPhaseSet

Overview

Group: VCF/BCF

Adds/fixes the phase set (PS) genotype field.

The VCF specification allows phased genotypes to be annotated with the PS (phase set) FORMAT field. The value should be a non-negative integer, corresponding to the position of the first variant in the phase set. Some tools will output a non-integer value, as well as describe this field as having non-Integer type in the VCF header. This tool will update the phase set (PS) FORMAT field to be VCF spec-compliant.

The handling of unphased genotypes with phase-sets is controlled by the -x option:

• If -x is used the genotype will be converted to a phased genotype (e.g. 0/1 => 0|1)
• Otherwise the phase-set (PS) will be removed from the genotype

The --keep-original option may be used to store the original PS value in a new OPS field. The type described in the header will match the original.

This tool cannot fix phased variants without a phase set, or phased variant sets who have different phase set values.

In some cases, VCFs (e.g. from GIAB/NIST or Platinum Genomes) have illegal header lines, for example, a PEDIGREE header line without a ID key-value field. The -z option can be used to remove those lines. This option is included in this tool for convenience as those example VCFs in some cases have these illegal header lines, and it is convenient to fix the phase set in addition to removing those illegal header lines.

Arguments

Name	Flag	Type	Description	Required?	Max # of Values	Default Value(s)
input	i	PathToVcf	Input VCF.	Required	1
output	o	PathToVcf	Output VCF.	Required	1
keep-original	k	Boolean	Store the original phase set in the OPS field.	Optional	1	false
phase-genotypes-with-phase-set	x	Boolean	Set unphased genotypes with a PS FORMAT value to be phased.	Optional	1	false
remove-no-id-header-lines	z	Boolean	Remove header lines that do not contain an ID key-value, which is required in VCF.	Optional	1	false