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?
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