This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
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?