PradoVarathan commented 4 years ago

Hi! This is an wonderful tool for PRS. Thank you so much. I just found that there might be a small error in one of the QC steps under standard GWAS QC step :

Alternatively, you can use R, with data.table v1.11.8+

library(data.table)

Read in file

dat <- fread("Height.gwas.txt.gz")

Filter out SNPs

result <- dat[INFO > 0.8 & MAF < 0.01]

Output the gz file

fwrite(result, "Height.gz", sep="\t")

Here, shouldnt the result be result = dat[INFO >0.8 & MAF > 0.01]

Thank you!

choishingwan commented 4 years ago

Yes, indeed. Nice spot! Thanks

On Sun, 26 Jul 2020 at 5:27 AM, Pradeep Varathan notifications@github.com wrote:

Hi! This is an wonderful tool for PRS. Thank you so much. I just found that there might be a small error in one of the QC steps under standard GWAS QC step : Alternatively, you can use R, with data.table v1.11.8+

library(data.table) Read in file

dat <- fread("Height.gwas.txt.gz") Filter out SNPs

result <- dat[INFO > 0.8 & MAF < 0.01] Output the gz file

fwrite(result, "Height.gz", sep="\t")

Here, shouldnt the result be result = dat[INFO >0.8 & MAF > 0.01]

Thank you!

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