Polyploidy found, and not supported by vcftools

Question

[sambioinfo2018]

Dear All,

I am getting the following error while running vcftools for polyploidy genome.

Error: Polyploidy found, and not supported by vcftools: 1A:3380

I ran the following script to see the polyploidy:

zgrep -v "^#"  sample.vcf.gz | cut -f 10- | cut -d ':' -f 1 | sort | uniq

And I get:

0/0/0/0/0/0
0/0/0/0/0/1
0/0/0/0/0/2
0/0/0/0/0/3
0/0/0/0/0/4
0/0/0/0/1/1
0/0/0/0/1/2
0/0/0/0/1/3
0/0/0/0/2/2
0/0/0/0/2/3
0/0/0/0/3/3
0/0/0/0/4/4
0/0/0/1/1/1
0/0/0/1/1/2
0/0/0/1/1/3
0/0/0/1/2/2
0/0/0/1/2/3
0/0/0/1/2/4
0/0/0/1/3/3
0/0/0/2/2/2
0/0/0/2/2/3
0/0/0/2/2/4
0/0/0/2/3/3
0/0/0/3/3/3
0/0/0/4/4/4
0/0/1/1/1/1
0/0/1/1/1/2
0/0/1/1/1/3
0/0/1/1/2/2
0/0/1/1/3/3
0/0/1/1/3/4
0/0/1/2/2/2
0/0/1/2/2/3
0/0/1/3/3/3
0/0/1/4/4/4
0/0/2/2/2/2

Could anyone suggest what could be the error?

Thanks!

[finswimmer]

Hello sambioinfo2018 ,

do you expect polyploidy in your samples?

If yes, than vcftoolsis obviously the wrong tool for whatever you like to do, as it statet clearly Polyploidy found, and not supported by vcftools. Tell us what you've tried to do, maybe one can recommend a better tool for it.

If no, than please tell us more about your data, what have you done to obtain the vcf file und what do you plan to do with it.

fin swimmer

[sambioinfo2018]

Hi Fins,

Thank you for your reply. Yes, the genome i am working is hexaploid. I have tried calling SNPs for the genome using freebayes software. I would like to filter the SNPs from the vcf file based on dept and quality of SNPs.

Thank you!

[finswimmer]

bcftools is what you are looking for.

E.g. bcftools view -i 'QUAL>40' input.vcf for getting all sites with QUAL > 40.

fin swimmer

[sambioinfo2018]

Thank you Fin for your suggestion.