Possible to remove .nosex IDs in Plink1.9
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6 weeks ago
salman_96 ▴ 30

Hi, In my fam file I have 4 individuals with no sex information. Is it possible to exclude them from downstream analysis. I have tried --allow-no-sex as well as --must-have-sex but they are kept in a .nosex file.

I am testing for interaction analysis in another tool with plink set of files

--allow-no-sex --must-have-sex plink1.9 • 226 views
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Thank you All. Appreciate it

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6 weeks ago

Two options:

  1. Use --remove on the .nosex file.
  2. Download plink 2.0, and use its --remove-nosex flag.
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6 weeks ago
arctic ▴ 30

Just to add to chrchang523's reply: If you know the sample IDs that you want to remove, you can make a list of those samples (with FID and IID as the first and second fields respectively, without the header) and then use the list to remove samples from the dataset.

plink --bfile inputdata --remove samplelist.txt --make-bed --out outputdata

PLINK link: https://www.cog-genomics.org/plink/1.9/filter

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6 weeks ago
salman_96 ▴ 30

Thankyou, I understand

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