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.
Alternate Alleles in VCF are more than 1 base
I've removed INDELS from a multi-sample vcf from HaplotypeCaller using SelectVariants. However, the ALT 'SNPs' are more than a single nucleotide substitution. Eg.
Q1) What is the meaning of the * symbol?
Q2) Is it to be expected that these SNPs are more than a single nucleotide substitution?