Specific information on HDS

[bgb-ipl]

Hi,

I need some information regarding the HDS output of Minimac4 (already discussed in the issue #26 ) : could you let me know if the HDS at two different variants can be considered independent ? For example, let's consider an individual and two variants (denoted SNPa with its 2 HDSs HDSa1/HDSa2 and SNPb with HDSb1/HDSb2). Could HDS be used to compute, for this individual, the dosage of the haplotype with the alternate alleles at both variants (denoted h11) using this formula:

h11 = HDSa1 * HDSb1 + HDSa2 * HDSb2 ?

If anything is unclear don't hesitate to let me know.

Thanks in advance,

[yukt]

You will need to consider LD structure. Variants can be correlated.

Best,

Ketian

On Wed, May 22, 2024 at 9:21 AM bgb-ipl @.***> wrote:

Hi,

I need some information regarding the HDS output of Minimac4 (already discussed in the issue #26 https://github.com/statgen/Minimac4/issues/26 ) : could you let me know if the HDS at two different variants can be considered independent ? For example, let's consider an individual and two variants (denoted SNPa with its 2 HDSs HDSa1/HDSa2 and SNPb with HDSb1/HDSb2). Could HDS be used to compute, for this individual, the dosage of the haplotype with the alternate alleles at both variants (denoted h11) using this formula:

h11 = HDSa1 * HDSb1 + HDSa2 * HDSb2 ?

If anything is unclear don't hesitate to let me know.

Thanks in advance,

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[bgb-ipl]

Thank you for your quick answer. Indeed if the HDS do not take the LD into account, the proposed formula is thus not correct.

Best,