Skip to content

Failed to select autosomal SNPs only (QC Step 3) #25

@Franklin593

Description

@Franklin593

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

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions