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!



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