How to deal polyploid and aneuploid sugarcane genome R570 for variant calling

Question

[analyst]

Dear Biostars community!

I have WGS data of hybrid variety (Saccharum officinarum and Saccharum spontaneum) of sugarcane R570. In variant calling step through GATK, I am stuck to set ploidy level of sugarcane because it contains varying number of chromosomes.

Please guide me how can i deal ploidy issue.

Thanks.

[dthorbur]

Is there any way to estimate ploidy from the supplier, or from the ancestors that established the hybrids?

I would suggest making an educated guess, continue with the analysis and when you get SNPs, you look at coverage and confidence of calls. Looking at how variation segregates in high SNP density regions can help inform if you've gotten it wrong or not. If ploidy is set too low, you'll likely see confident SNPs in the BAM not being called, and if you get it too high, you might get low confidence calls.