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?