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.
Too much varients
We did exome sequencing to one person and run it through GATK best practice pipeline (used Haplotype Caller) combined with 10 samples which I have downloaded from 1000 Genomes project (as recommended). It's Appear that my sample have around 450,000~ SNVs. Is it normal result??
We also analyzed this sample using BGI(china) services (not sure which pipeline they have used, unfortunately) and we VCF file with only 35,000 SNVs..
Is there a problem my analysis?