downlaod snp from UK Biobank imputed snp chr1 ukb22828 file
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?
• 2,217 views
•
link
updated
by
Mathias
•
written
by
stevenlehrer •
•
written
by
stevenlehrer •
1 answer
use the option -incl-rsids
https://www.well.ox.ac.uk/~gav/qctool_v2/documentation/alphabetical_options.html
Log in to answer this question.
More posts like this
-
Highly inflated p-values in GWAS by regenie
written by cwwong13 •
-
How can I keep INFO value when convert bgen to VCF by using plink2?
written by MHSATO •
-
qctool to merge two bgen file fails with no clear reason to
written by kpatil •
-
Plink 2 user error converting .bgen to bcf
written by Salahuddin •
-
formatting error: Calculate LD matrix from bgen file
written by chrisclarkson100
-
extract list of SNPs from multiple chr{1:22}.bgen files using plink2
written by Sharad •
-
Merge bgen,bgen.bgi,and .sample file from uk biobank
written by okiedokie1208 •
-
Plink bim from bgen
written by meggo •
-
Strands are reversed
written by richyanicky •
-
plink2 bgen to vcf ukbiobank
written by richyanicky •
What's the output log saying? Use qctool2, subsetting a single SNP is going to be a whole lot faster.
No error message on log, just keeps running. After 5 hrs I stopped process.
I want to get eids of all subjects with variant snp. If I subset for a single individual, how do I get the rest?
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