PLINK: ERROR: No nonmissing markers for individuals when using --cluster

Question

[hemr3]

Sorry if this is a repeat question - but all the answers I could find didn't help.

This is the error:

ERROR: No nonmissing markers for individuals Ind1 Ind1 - Ind2 Ind2

Here are the steps I have done:

Convert .vcf to plink format (ped, map) and then to binary format (bim bam bed):

vcftools --vcf data.vcf --plink --out data

plink --file data.vcf --noweb --make-bed --recode --missing-genotype 0 --out data

This is where the error occurs:

plink1 --bfile data.vcf --cluster --noweb

I have tried to make another .clust file using:

bcftools query -l data.vcf.gz | awk '{split($1,pop,"."); print $1"\t"$1"\t"pop[2]}' > data.clust

Which looks like this:

Ind1    Ind1    
Ind2    Ind2
Ind3    Ind3

But using this file results in the error:

Reading clusters from [ data.clust ]
Ind1 Ind1 

ERROR: Problem reading from [ data.vcf.clust ]

I am preparing vcf files for TreeMix analysis, and these genome files do have a high-degree of missingness, if that makes a difference.

The original .vcf file looks like this:

##FORMAT=<ID=GT,Number=1,Type=String,Description="Unphased Genotype">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  Deni4   Mez1
22  17049382    .   C   T   .   PASS    .   GT  ./. ./.

I'd be very grateful for any help!

[chrchang523]

1. You aren't accurately reporting the commands you ran. plink --file data.vcf ... won't work after vcftools --vcf data.vcf --plink --out data. You ran something slightly different, and for any troubleshooting question it is often critical for you to post EXACTLY what you ran.
2. Both vcftools and plink 1.07 have been obsolete for years. vcftools --plink is less reliable, much slower, and throws away more information than plink 1.9 --vcf.
3. plink's --mind flag can be used to filter out samples with too many missing genotypes.

[hemr3]

Thank you for your help! But I did run those commands, and they did work - but maybe they worked in a sort of janky way that made the files difficult/impossible to deal with. I'll update plink and try the --mind flag!

[chrchang523]

If it worked, it would be because the second command read DIFFERENT (preexisting) files than what your first command generated.