A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing.

Using the complete variant dataset, we found a highly significant difference in the distribution of distances between intra-individual and inter-individual samples (Wilcoxon test, HaplotypeCaller: p = 1.31 × 10 –28 , Mutect2: p = 1.51 × 10 –28 ) ( Figure 5B ).

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