Re: How to calculate dosage data missing rate from arg --missing？

[Matthew Maher]

to get any of the optional columns, you need to ask for them via a cols=   option

See: https://www.cog-genomics.org/plink/2.0/general_usage#colset

On Mon, Jul 8, 2024 at 8:03 AM Wentao Yao <wenta...@foxmail.com> wrote:

Hi, now I have the dosage gene data in bpfile format. However, when I try to calculate the dosage data missing rate by plink2 --missing, I find that only output the hard-called missing rate. But I saw that the plink2 wiki said " By default, this summarizes hardcall missingness. There are optional output columns summarizing dosage missingness, as well as heterozygous haploid (including mixed MT) counts", and "FILE FORMAT" section also said the output file will have a column named " MISSING_DOSAGE_CT". But in my output file, I have not seen this column, it only have "MISSING_CT". I'm not sure if I missed something.

I am looking forward to your reply, thanks!

--
You received this message because you are subscribed to the Google Groups "plink2-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to plink2-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/plink2-users/1da48987-39e2-414e-8b5d-c092f10c4ed0n%40googlegroups.com.