how to count the numbers of SNPs per sample?
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12 months ago
nayeona.hi ▴ 50

Hello, this is my first data analysis with PED and MAP file.

I started on Plink, first with tutorials.
I generated bim, fam and bed files from PED and MAP files,
the total number of samples is 6674 and I checked in the fam file.
What I wonder is how can I check the SNPs per sample?
In the bim file, there are 352227 rows of SNPs, is it right those SNPs are all in one sample in common?

I also generated raw file through "-recodeAD" and the size is too big to read in R (on Ubuntu).
Is there any method to split the file or some other tips to make smaller from the first?

Help for the first step, please.
Or let me know where I can refer to.

Thank you

SNP plink bim_file • 371 views
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Entering edit mode
12 months ago
Sam ★ 3.5k

If you want to know the genotyping rate for each individual, then you can use plink --bfile <ped prefix> --missing

and the information can be found in the imiss file.