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.
Why so few PASS variants?
I was trying to run the GenomeStrip with 30 high-coverage samples using Discovery->Genotyping processing pipeline. It run successfully but the final vcf had so few PASS sites, like chr21 only 70 DELs left. In the 1000genome phase3 vcf, there is over 300 DELs in chr21.
I are running the SV preprocessing, discovery and genotyping processes separately on each chromosome. I am afraid that if it is because I made the metadata on each chromosome, not the whole genome? Could you help me？