GATK HaplotypeCaller sensitivity and precision are close between the three methods, with small trade offs for different methods. For SNPs, pooled calling is most sensitive at the cost of more false positives, and single calling is more precise at the cost of some sensitivity. Joint calling is intermediate between these two extremes. For indels, joint calling is the most sensitive at the cost of more false positives, with pooled calling falling between joint and single sample calling.

Incremental joint variant calling Variant calling in large populations is challenging due to the difficulty in providing a consistent set of calls at all possible variable positions. A finalized se…

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