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.
DepthOfCoverage, QualifyMissingIntervals and DiagnoseTargets?
I using GATK for Clinical Whole-Exome Sequencing. I often have to answer questions for evaluating quality the sequencing run:
- How good is my genes of interested covered?
- Which exons are not well covered?
- Which interval are not well covered?.
I've tried several tools which try to address this question (i.e. bcbio-nextgen, chanjo). But now I have a feeling that the tools (mentioned in the title) can answer more or less my questions, except the nice feature of
chajo which allows storing/querying statistics across samples.
My question about these tools: When to use which?
From the names and reading description of their command line arguments, I can't answer the question clearly. I tend to try all three in this order:
DepthOfCoverage -> QualifyMissingIntervals -> DiagnoseTargets.
So again, when to use which?