Hi,

I am using Freebayes to call variants on a genome of unknown ploidy.

I only applied the -p parameter in the command line (starting with 1 and 2, to check the obtained results), which has identified many variants. In fact, from what I've read, it is better to not apply any parameter and then filter the variants afterwards.

But then, are there any best-practice filtering steps to reduce the high number of variants identified? I'm thinking about the coverage levels, the minimum mapping quality and so on. Would this depend on the ploidy level?

Any suggestion will be greatly appreciated!

Thanks

Barbara