I have previously performing Allelic scoring in Plink 1.9 using:
plink \
--score sum sumstats.txt\
However, it seems this has changed in Plink 2.0. What is the equivalent function for Allelic scoring?
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2 Answers
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plink2 --score cols=+scoresums
See https://www.cog-genomics.org/plink/2.0/general_usage#colset and https://www.cog-genomics.org/plink/2.0/score for details.
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I don't have enough reputation for a comment but the place where the option to add scoresums is listed is here https://www.cog-genomics.org/plink/2.0/formats#sscore
