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.
missing rs IDs in VCF file using samtools, what is the best tool from GATK?
Used samtools, mpileup and got raw.vcf but the rs ID are missing instead there are dots under the rs ID column. Can I process the same file further with a GATK tool and get the snps? or should I process the .sorted.ba, files again with a GATK?
I also want to be able to distinguish somatic vs germline cells, what is best tool for that?