Specifics of -j 3 option

[slcapel]

Hello, I was hoping you could tell me which Jacquard states are implemented when setting -j 3. I also notice that when I implement -j 3, the last 4 columns of out.kin.gz do not sum to column 4.

[haplotype]

in table 1 of the manuscript (can be found here https://www.biorxiv.org/content/10.1101/2023.09.02.556031v1.full.pdf) -j 3 assume loadings from \Sigma 1-6 are 0 and only considers \Sigma 7,8,9, which are Jacquard states of no inbreeding.

Grant

On Wed, Dec 20, 2023 at 6:21 PM Samantha Capel @.***> wrote:

Hello, I was hoping you could tell me which Jacquard states are implemented when setting -j 3. Thank you.

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[slcapel]

Thank you! Is the Supplement that pairs with the manuscript available? I can't seem to find it on bioRxiv.

[haplotype]

oh. I just uploaded both manuscript and supplementary here at github. the supplementary can be found here: https://github.com/haplotype/kindred/blob/main/kindred-supp.pdf

Grant

On Thu, Dec 21, 2023 at 3:42 PM Samantha Capel @.***> wrote:

Thank you! Is the Supplement that pairs with the manuscript available? I can't seem to find it on bioRxiv.

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