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.
Homo_sapiens_assembly19.kown_indels.vcf vs. Mills_and_1000G_gold_standard.indels.hg19.sites.vcf
Have a long standing stable pipeline, which I need to tweak as can be explained and justified.
What is the difference between the old file of known indels (from Mills paper(s)) - Homo_sapiens_assembly19.kown_indels.vcf
And the current version of known indels with 1000G added - Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz
I know the newer reference is smaller - just sites. It also has significantly fewer records/line counts. What else was removed or added from the old version until now?
Thanks in advance.