Check for duplicates and determine sex from the VCF in a cohort of about 110 patients

Question

[Gl_14]

Hello,

I have the VCF of about 110 patients and I would like to:

• check for duplicates
• determine their sex

Is there someone who knows how to use KING (https://people.virginia.edu/~wc9c/KING/) that could help me with the correct commands?

We tried to use it, but we got stuck at the conversion .vcf-->.bed files.

Or are there other software to do this?

Thank you

[Ram]

AFAIK, KING does kinship analyses. Have you tried using plink --check-sex? There are other plink commands that can help you find duplicates (although KING might be useful here - you are, after all, looking for predictions for identical twins that are in reality duplicates)

[Gl_14]

For determining the sex: We tried to use plink --check-sex, but it did not give us an output (Determine the sex of a sample from a .vcf this was me), could you please tell me what to write in the terminal to use this command?

To check for duplicates: which are the other plink commands, if you know any? (yes they suggested us to use KING for this reason)

Thanks

[chrchang523]

You misconfigured your system PATH relative to where you placed the plink 1.9 binary, and some other binary also named "plink". When you have fixed this, plink --version will tell you that you are running plink 1.9.

[Ram]

From your previous post, it looks like you may not have plink installed properly. Try the steps from the Getting Started section and ensure the right version of plink is installed properly.

it did not give us output

Something smells fishy. Tools will either error out or give some sort of output.