Setting ploidy level in gatk

Dear all,

i am working on sugarcane WGS analysis. I downloaded reference genome SofficinarumxspontaneumR570 from phytozomev13. In variant calling step i do not know which ploidy should i set in haplotypecaller as sugarcane is anueploid.

Please guide about ploidy level of sugarcane hybrid variety SofficinarumxspontaneumR570.

Thanks alot.

ploidy

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written 1.5 years ago by Bushra Bibi

1 answer

Have you seen: https://gatk.broadinstitute.org/hc/en-us/articles/360035889691-Does-GATK-work-on-non-diploid-organisms

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written 1.5 years ago by GenoMax

I will look into it thanks!

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written 1.5 years ago by Bushra Bibi

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