Hi,

I ran CRISP to do the variant calling in some Drosophila pooled samples and when I try to filter for minimum allele frequency with vcftools I get the following error:


    VCFtools - 0.1.14
    (C) Adam Auton and Anthony Marcketta 2009

    Parameters as interpreted:
    	--vcf new_variantcalls.vcf
    	--maf 0.15
    	--out berg

    After filtering, kept 14 out of 14 Individuals
    Error: Polyploidy found, and not supported by vcftools: YHet:49

Does anybody know how to fix this?


I run the grep command Pierre suggested and this is the output is here: https://jpst.it/MUgG
looking at the vcftools source code: https://github.com/kiwiroy/vcftools/blob/master/cpp/vcf_entry_setters.cpp#L97


    		if (pos != pos2)
    LOG.error("Polyploidy found, and not supported by vcftools: " + CHROM + ":" + header::int2str(POS));


you have a strange genotype in CHROM=  YHet at POS = 49. (something that doesn't look like '([0-9]+/[0-9]+)'.
I suppose you have more than two alleles for a Genotype 

please, show us the output of 

     grep -v "^#"  new_variantcalls.vcf | cut -f 10- | cut -d ':' -f 1 | sort | uniq

> Does anybody know how to fix this?

change the way your VCF is called. ...


