Question: Problem using plink file with ADMIXTURE
1
gravatar for beneficii
3.9 years ago by
beneficii60
beneficii60 wrote:

I had my whole genome sequenced. In plink, I put the VCF file through and it produced 3 files: plink.bed, plink.bim, and plink.fam. As recommended by Sam in another comment, I made a backup of plink.bim and ran this Linux command on the backup: "sed 's/^chrM\s/25\t/g; s/^chrX\s/23\t/g; s/^chrY\s/24\t/g; s/^chr//g' plink-backup.bim > plink.bim" With this the changes are reflected in the file plink.bim. I then run admixture "./admixture -j2 plink.bed 4" and I got this error:

**

Error: detected that all genotypes are missing for a SNP locus.
Please apply quality-control filters to remove such loci.

**

I have no idea what to do at this point.

linux plink admixture genome • 3.0k views
ADD COMMENTlink modified 3.9 years ago by Philipp Bayer6.9k • written 3.9 years ago by beneficii60
2
gravatar for Philipp Bayer
3.9 years ago by
Philipp Bayer6.9k
Australia/Perth/UWA
Philipp Bayer6.9k wrote:

So it sounds like one of your SNPs has all alleles missing, which is likely to happen if you've got only one genome there (yours).

You can remove SNPs that have missing alleles using plink

plink --geno 0.1 --file your_file --recode --out your_filtered_file

geno 0.1 means 'remove variants with missing call rates exceeding the provided value (default 0.1)', 0.1 (10%) should be more than enough for your case since your missing rate is 1.0 (100%)

This should print how many SNPs have been filtered out.

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by Philipp Bayer6.9k

And should I do this on the BIM file, or the BED file?

ADD REPLYlink written 3.9 years ago by beneficii60

Ah sorry, you have bed/bim/fam -

so run it like this:

 plink --geno 0.1 --bfile plink --recode --out your_filtered_file

The --bfile flag will assume that you have files starting with 'plink' and ending in '.bed', 'bim', 'fam'

ADD REPLYlink written 3.9 years ago by Philipp Bayer6.9k

Thank you much! It's running now with no errors.

ADD REPLYlink written 3.9 years ago by beneficii60
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