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.
Max Alt Alleles behavior
I'm using HaplotypeCaller to call a vcf file with 8 samples. I left the --max_Alt_Alleles argument at its default 6. However I'm getting some odd warning messages:
WARN 19:12:58,670 ExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at chr1:2274306 has 26 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
Since I'm calling 8 samples, shouldn't the maximum number of alternate alleles be 15 (2n-1)? Or is the number of alternate alleles observed in the given context referring to the number of possible haplotypes that could possibly be constructed from the aligned reads?