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.
General variant detection pipeline
I'm a bit uncertain as to the optimal pipeline for calling variants. I've sequenced a population sample of ~200 at high coverage ~30X, with no prior information on nucleotide variation.
The most rigorous pipeline would seem to be:
1. Call variants with UG on 'raw' (realigned) bams.
2. Extract out high-confidence variants (high QUAL, high DP, not near indels or repeats, high MAF)
3. Perform BQSR using the high-confidence variants.
4. Call variants with HaplotypeCaller on recalibrated bams.
5. Perform VQSR using high-confidence variants.
6. Any other hard filters.
Is this excessive? Does using HaplotypeCaller negate the use of *QSR? Is it worthwhile performing VQSR if BQSR hasn't been done? Otherwise I'm just running HaplotyperCaller on un-recalibrated bams, and then hard-filtering.