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Update tutorial.rst
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AlexTISYoung authored Sep 21, 2023
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Expand Up @@ -94,7 +94,7 @@ To perform imputation from the phased .bgen file in example_data/, use the follo

``impute.py --ibd [email protected] --bgen chr_@ --king king.kin0 --agesex agesex.txt --out chr_@ --threads 4``

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.

Family based GWAS
-----------------
Expand Down Expand Up @@ -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.

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