If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
what is max-alternate-alleles ?
firstly ,set max-alternate-alleles is 6 .
I guess max-alternate-alleles means that at a site , the ref allele is A , the number of other alleles type (C,G) found by reads do not more than 6 . but as we know , just total 4 base types : A,T,C ,G , so I think the max-alternate allele will count indel at a region ,not a point putation.
the max-alternate-alleles setting only is available for indel region ,rather than point mutaion site .
Am I right ?