Extract list of rsIDs from plink

Question

[samuel]

I have a huge vcf file that I needed to update the SNP names from position (chr1-22:xxxxxx) to rs name in VCF file.

I used SnpSift as suggested here: updating SNP names in VCF file

Now the vcf contains chrme.position AND rsID like so:

22      16050783        22:16050783:A:G;rs587743568     A       G       .       .

I make .bed, .bim and .fam files in plink as I need to do plink analysis like so:

plink --vcf  after.SnpSift.vcf.gz --double-id --keep-allele-order --make-bed  --out my.plink.data

I now want to extract a list of rsIDs from the bed file like what was suggested here: Plink: Retrieving specific SNP data for individuals in dataset

If my snps.txt is just the rs ID like so:

cat snps.txt
rs587743568

My command fails:

plink --bfile my.plink.data --extract snps.txt --recodeA
Error: No variants remaining after --extract.

If my snps.txt is chrme,position and rsID it works e.g

cat snps.txt
22:16050783:A:G;rs587743568

plink --bfile my.plink.data --extract snps.txt --recodeA
--extract: 1 variant remaining

However, I need for this to work with just using the rsIDs. Can anyone help?

Answer 1

[zx8754]

Update the SNP names first, then you can subset using new names: --update-name <filename>