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.
Is UnifiedGenotyper actually better than HaplotypeCaller for this pooled sample project?
Hi, I am interested in calling variants from pooled samples. Specifically, I wish to determine SNP allele frequencies from samples that were made by pooling many individuals (1000+) together. I know that HaplotypeCaller is now recommended over UnifiedGenotyper in all cases. However, is this project an exception? I have:
- 1000s of individuals in each pooled sample
- only two possible alleles at every site
- I only need to call SNPs
- I can generate a set of known SNPs to call (does GENOTYPE_GIVEN_ALLELES work in HaplotypeCaller?)
- I have high read coverage
- I want to detect rare alleles as best as possible
If you still advise using HaplotypeCaller in this case, do you have any special suggestions? I'd like to maximize the -ploidy number to detect the rare alleles, but otherwise streamline the job. Thanks for any advice you can provide!