Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
CombineGVCFs / GenotypeGVCFs and ploidy
I am setting up a pipeline for HaplotypeCaller and there is something I do not understand. In the manual pages of CombineGVCFs and GenotypeGVCFs it is said: "This tool is able to handle any ploidy (or mix of ploidies) intelligently; there is no need to specify ploidy for non-diploid organisms".
But then there is the description of the "--sample_ploidy" argument. Do I have to set the number of samples?
And if I want to genotype the X chromosome for a set of samples (for which, depending on the sex, HC was run with ploidy 1 or ploidy 2), do I have to do something special?