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.
ALT field in vcf is a *
My variant call set contains SNP calls which have a "*" listed as alternative allele (field 5 in the vcf) which isn't specified in the vcf specifications. I have noticed that they generally appear in short series on a chromosome (e.g. positions 109-115). Are these positions indicative of indels?