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@@ -94,7 +94,7 @@ To perform imputation from the phased .bgen file in example_data/, use the follo | |
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``impute.py --ibd [email protected] --bgen chr_@ --king king.kin0 --agesex agesex.txt --out chr_@ --threads 4`` | ||
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As with the ibd.py script, the impute_runner.py script can use a user input :ref:`pedigree file <pedigree>` (with the *--pedigree* argument) rather than the *--king* and *--agesex* arguments. | ||
As with the ibd.py script, the impute.py script can use a user input :ref:`pedigree file <pedigree>` (with the *--pedigree* argument) rather than the *--king* and *--agesex* arguments. | ||
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Family based GWAS | ||
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@@ -186,4 +186,4 @@ For an exercise involving polygenic score analysis, please see the :ref:`Simulat | |
.. then imputed paternal and maternal PGS are perfectly correlated, | ||
.. and the above regression on proband, paternal, and maternal PGS becomes collinear. | ||
.. To deal with this, add the --parsum option to the above command, | ||
.. which will estimate the average NTC rather than separate maternal and paternal NTCs. | ||
.. which will estimate the average NTC rather than separate maternal and paternal NTCs. |