--absent-to-ref and --unspecified-to-ref

[BinglanLi]

• Do you want to request a feature or report a bug?

feature

• What is the current behavior?

There is only --missing-to-ref feature at the moment and it confuses a few situations

• For multi-sample VCFs,
  • If a position is absent in the VCF, set it to reference.
  • If every sample has ./. at a position, set it to reference.
  • If some samples have ./. and the rest have specified genotype calls, do nothing
• For single-sample VCFs
  • No different between absent or ./.. Everything will be set to reference.

• What is the expected behavior?

--missing-to-ref

• If a position is absent in the input VCF, add it back as 0/0
--unspecified-to-ref
• convert any ./. to 0/0

• What is the motivation / use case for changing the behavior?

Differentiate the behaviors towards absent vs known missing genotypes. The latter can be due to quality issues and should not be set to reference.

[markwoon]

Released in 3.0