downlaod snp from UK Biobank imputed snp chr1 ukb22828 file
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11 weeks ago
stevenlehrer ▴ 10

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?

speed • 293 views
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What's the output log saying? Use qctool2, subsetting a single SNP is going to be a whole lot faster.

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

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

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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

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