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Author: Subject: --unrelated not reporting individuals to remove
prussell0
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[*] posted on 10/19/2021 at 03:09 PM
--unrelated not reporting individuals to remove


Hi,

I am trying to use KING 2.2.7 with `--unrelated` to generate a list of individuals with relatives to remove. When using `--related`, KING identifies many pairs of individuals at the given relatedness level. However, when using `--unrelated`, it only identifies one individual to remove. I have verified that the pairs of related individuals include a variety of individuals.

Here is a small example. The same happens for other relationship degrees as well.

Code:
$ king -b dataset.bed --related --degree 5 $ wc -l king.kin0 266 king.kin0 $ king -b dataset.bed --unrelated --degree 5 $ wc -l kingunrelated_toberemoved.txt 1 kingunrelated_toberemoved.txt $ king -b dataset.bed --unrelated --degree 6 $ wc -l kingunrelated_toberemoved.txt 1 kingunrelated_toberemoved.txt


Do you know what is happening here?

Thanks,
Pam
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prussell0
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[*] posted on 10/21/2021 at 03:51 PM


I just discovered why I am seeing this behavior. For `--unrelated`, if `--degree` is greater than 2, the program switches to 2 as higher degrees are not supported. I would like to suggest that the program crash with a helpful error message rather than running through with this information mentioned among the output. Thank you!
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theKING
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[*] posted on 11/3/2021 at 03:58 PM


I am glad that you have discovered yourself that KING --unrelated can only extract a subset that is unrelated up to the second-degree. If you would like to remove further relatedness, you can run king --ibdseg --degree 5 with the generated subset, and then remove further relatedness. Thanks for the "let crash" suggestion, and we will decide on a better way to handle it, e.g., making the warning message even more obvious than now.
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