MareesAT / GWA_tutorial

A comprehensive tutorial about GWAS and PRS

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Failed to select autosomal SNPs only (QC Step 3)

Franklin593 opened this issue · comments

While running:

# Select autosomal SNPs only (i.e., from chromosomes 1 to 22).
awk '{ if ($1 >= 1 && $1 <= 22) print $2 }' HapMap_3_r3_6.bim > snp_1_22.txt
plink --bfile HapMap_3_r3_6 --extract snp_1_22.txt --make-bed --out HapMap_3_r3_7

Here are the error logs:

PLINK v1.90b7.2 64-bit (11 Dec 2023)           www.cog-genomics.org/plink/1.9/
(C) 2005-2023 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to HapMap_3_r3_7.log.
Options in effect:
  --bfile HapMap_3_r3_6
  --extract snp_1_22.txt
  --make-bed
  --out HapMap_3_r3_7

16125 MB RAM detected; reserving 8062 MB for main workspace.
1430443 variants loaded from .bim file.
165 people (81 males, 84 females) loaded from .fam.
112 phenotype values loaded from .fam.
Error: No variants remaining after --extract.

Here are the HapMap_3_r3_6.bim:

1	rs2185539	0	556738	T	C
1	rs11240767	0	718814	T	C
1	rs3131972	0	742584	A	G
1	rs3131969	0	744045	A	G
1	rs1048488	0	750775	C	T

Here are the snp_1_22.txt

rs2185539
rs11240767
rs3131972
rs3131969
rs1048488

I have searched through Google and documents, but still haven't found a solution.
Your input or guidance on this would be highly appreciated