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.
Flagging Low Coverage Regions for Alternate Reference Maker
I am currently working on a comparative genomics project which involves using NGS datasets to map reads from several closely related species to a reference genome. I'd like to produce alternate fasta files for each species incorporating SNPs discovered using the GATK pipeline. Due to the experimental design I expect that there are regions in the genome that have low coverage, therefore I'd like to have a way to designate a base position as "N" if the read depth at that position does not meet a specified threshold. I found some tools to do diagnostic evaluation of coverage depth, but I couldn't find out a tool that would incorporate low coverage into the output fasta file produced by a tool such as FastaAlternateReferenceMaker. Thanks in advance!