If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
input.genomeSize affects calls GenomeSRiP calls?
I am wondering if the parameter input.genomeSize in the config file affects the CNV calls. I am trying to make calls on chromosome 22, at the beginning I set input.genomeSize=51304566, the program complains that there is no data (or the data is empty something like that). This value contains all the Ns in the chromosome 22. Then I set the input.genomeSize=34894566 (which copied somewhere on the internet). Then the program went through. I did not change anything else (except input.genomeSizeMale and input.genomeSizeFemale were set accordingly).
Does this parameter really affect the calls? And I want to make calls by chromosome, I have to prepare a config file for each chromsome?