downlaod snp from UK Biobank imputed snp chr1 ukb22828 file

Question

[stevenlehrer]

I am using this code

plink2 --bgen ukb22828_c1_b0_v3.bgen ref-first --sample ukb22828_c1_b0_v3.sample --snp  rs1284368 --make-bed --out  rs1284368

After 5 hrs still no output. How can I speed this up?

[4galaxy77]

What's the output log saying? Use qctool2, subsetting a single SNP is going to be a whole lot faster.

[stevenlehrer]

No error message on log, just keeps running. After 5 hrs I stopped process.

[stevenlehrer]

I want to get eids of all subjects with variant snp. If I subset for a single individual, how do I get the rest?

[stevenlehrer]

Here is command line qctool -g ukb22828_c1_b0_v3.bgen -s ukb22828_c1_b0_v3.sample -og filtered.bgen I want only rs1284368 How do I alter command line

Answer 1

[Mathias]

use the option -incl-rsids

https://www.well.ox.ac.uk/~gav/qctool_v2/documentation/alphabetical_options.html