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.
Ploidy parameter in UnifiedGenotyper
I just want to know what you mean by "-ploidy" in UnifiedGenotyper.
--sample_ploidy / -ploidy ( int with default value 2 )
Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy).
I am working on an inbred (homozygous) strain of mice. I have only one sample. Should I use number 2 here that represents the diploid nature of the genome. I am confused as it says Ploidy (number of chromosomes) per sample.