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Xpar option missing for IMPUTE4 #3
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Hi Eyherabh, Sorry that line was commented out. Regarding the effective size, you would check the reference stated in IMPUTE2: Best, |
Thanks. I know that the impute4 manual does not list the -chrX flag. However, the manual does not inspire too much confidence since both it has typos that render the example there non-working, and the flag -chrX is acknowledge when passed to impute4. The publication where impute4 was introduced (https://www.nature.com/articles/s41586-018-0579-z) does not clarify matters further really. The methods section states that PAR and non-PAR regions were, after some filtering, processed analogously to the autosomal regions, which were imputed with impute4. |
The file
R/phasingImpute4.R
has the comment## impute for chrX PAR >> with an additional flag: --Xpar.
However, the lines following it and running IMPUTE4 do not have that flag set, i.e.
Could you please clarify whether the effectiveSize is being reduced elsewhere in order to mimic the effect of the missing flag as per IMPUTE2?
Thanks
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