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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.
Maximizing sensitivity of HaplotypeCaller for pooled sample
I'm attempting to call variants (primarily SNPs) with HaplotypeCaller from a pooled sample containing 95% wild-type and 5% polymorphic strain data (C. elegans, SE-50bp, 20-fold genomes). Per guidelines, the '''-ploidy 40''' flag was used, but it's only detecting ~1/4 the number of SNPs as other variant callers (e.g., FreeBayes and VarScan2). I can validate by prior annotation (the polymorphic strain has been sequenced) so I'm not concerned about false-positives. What additional parameters should be used to increase sensitivity?