merging diploid and tetraploid vcfs

Question

[analyst]

Hi,

I have constructed single de novo assembly of two varieties diploid and tetraploid. Later on, variants are called for diploid and tetraploid variety. Now i have two merged vcf files one representing diploid variety and other tetraploid variety. Can I further merge both diploid and tetraploid files into one through bcftools without losing ploidy information? Please guide.

Thankyou

[colindaven]

How are you calling tetraploid variants out of interest ?

[analyst]

I used freebayes for variant calling setting --ploidy 4 for tetraploid samples and --ploidy 2 for diploid samples.