Ignore typed SNPs not present on reference panel?

[biona001]

Currently, all typed SNPs must be present on the reference panel. This ensures that all output genotypes can be phased.

If we do not insist on outputting phased data, we should add an option so that MendelImpute automatically ignores those typed SNPs and just output them.

[anamnazir1]

Hi ! Benjamin Chu

I am reproducing your code i have a quick question regarding haplotypes selection during window 1,2,3,4 etc

In Fig 1d, we have candidate haplotypes (h1,h2,h3), (h4,h5,h6) in window 1, but in window 2 how h3 is replaced with h6, h4 is dropped, and h7,h8 are selected, please explain the criteria for haplotype selection during windows and how h1 and h5 is selected as phased haplotypes in window 1 although h1,h2 and h3 are same.

[biona001]

@anamnazir1 I responded to your email separately, let me know if you didn't get it. In the future, please open a new issue for questions not related to the original issue. Thank you!