Hello all,

I would like to remove any singletons/doubletons from my vcf file.

I can find all the singletons/doubletons using: `vcftools --vcf file.vcf --singletons --out file` 

This output `file.singletons` which has this information:
`CHROM   POS     SINGLETON/DOUBLETON     ALLELE  INDV`

I thought I could extract the `POS` column from the `file.singletons`, remove the header and use as follow:

`vcftools --vcf file.vcf --exclude file.singletons --recode --recode-INFO-all --out final_vcf`

However this does not seem to remove any SNPs from the `.vcf` file. Is there anyway I can remove the SNPs listed in the `.singletons` file?

Thank you all for your help in advance 
 
If anyone is having a similar problem - I found the solution!
Instead of using `--exclude` flag use the `--exclude-positions` flag for `vcftools`. Make sure you take the 1st and second column of the `--singletons` output.