Question: Full list of KING options and paramenters
0
gravatar for gaelgarcia05
10 months ago by
gaelgarcia05190
UK
gaelgarcia05190 wrote:

I'm trying to understand all the options and parameters that KING supports, but I can't find a complete list of this anywhere.

The manual / tutorial is the closest thing I have, but even then, it's pretty scattered and I suspect not all options are mentioned.

Does anyone know where is a good place to obtain this list?

Thanks!

ibd plink kinship relatedness king • 487 views
ADD COMMENTlink modified 8 months ago by Wei-Min Chen0 • written 10 months ago by gaelgarcia05190
1
gravatar for gaelgarcia05
10 months ago by
gaelgarcia05190
UK
gaelgarcia05190 wrote:

UPDATE:

It turns out that once you can actually get KING running, one of the things it returns is a consolidated list of its options:

KING 2.1.3 - (c) 2010-2018 Wei-Min Chen

The following parameters are in effect:
                   Binary File :    ../ex/ex.bed (-bname)

Additional Options
         Close Relative Inference : --related, --duplicate
   Pairwise Relatedness Inference : --kinship, --ibdseg, --ibs, --homog
              Inference Parameter : --degree
         Relationship Application : --unrelated, --cluster, --build
                        QC Report : --bysample, --bySNP, --roh, --autoQC
                     QC Parameter : --callrateN, --callrateM
             Population Structure : --pca, --mds
              Structure Parameter : --projection
              Disease Association : --tdt
   Quantitative Trait Association : --mtscore
                Association Model : --trait [], --covariate []
            Association Parameter : --invnorm, --maxP
               Genetic Risk Score : --risk, --model [], --prevalence, --noflip
              Computing Parameter : --cpus
                   Optional Input : --fam [], --bim []
                           Output : --prefix [king], --rplot


Please specify one of the following 18 options: --related --kinship --autoQC --mtscore --risk --ibs --homog --ibdseg --mds --pca --cluster --build --bysample --bysnp --tdt --unrelated --duplicate --roh
ADD COMMENTlink modified 10 months ago • written 10 months ago by gaelgarcia05190
0
gravatar for Wei-Min Chen
8 months ago by
University of Virginia
Wei-Min Chen0 wrote:

The updated KING tutorial (http://people.virginia.edu/~wc9c/KING/manual.html) is now more detailed, with options and parameters listed in the left panel

ADD COMMENTlink written 8 months ago by Wei-Min Chen0
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