We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.
GATK 184.108.40.206, human WES
I'm using HaplotypeCaller with the -ploidy option for the sex chromosomes:
Male: chr1-22 = ploidy 2
Male: chrX,Y = ploidy 1
Female: chr1-22,X = ploidy 2
With the MergeVcfs I merge the two male gvcfs to one and then I join my cohort gvcfs (males and females samples) with GenomicsDBImport and at the end I'm going to use GenotypeGVCFs.
I cann't figure out how to calculate the ploidy value to set up with GenotypeGVCFs. What is the meaning of "pool" in my case? My male gvcfs have a mixed ploidy. I have to change strategy? I have 50 male and 55 female samples.
> ---------------------------- > --sample_ploidy / -ploidy > Ploidy per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy). > Sample ploidy - equivalent to number of chromosome copies per pool. For pooled experiments this should be set to the number of samples in pool multiplied by individual sample ploidy. > ----------------------------