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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.
RNA-Seq variants from 2-step alignments
Thank you for providing guidelines on RNA-Seq variant discovery. For our data, we are currently playing with multiple mapping methods and have noticed that 2-step alignments work "better" than 1-step alignments. By 2-step alignments, I mean using STAR as step1 and then take the unmapped from this and use another aligner (like Bowtie2) for alignment. If I use such a methodology, will there be an issue in variant calling when during splitting cigar strings I ask it convert the 255 MAPQ to another value (like 60 in the best practices example), since bowtie2 gives different MAPQ scores. Sorry if this seems like a stupid question, but I am just a little curious how such a thing might affect the variant calls. Any insights/comment on this will be greatly appreciated.