Bam-readcount - rapid generation of basepair-resolution sequence metrics

Bam-readcount is a utility for generating low-level information about sequencing data at specific nucleotide positions. Originally designed to help filter genomic mutation calls, the metrics it outputs are useful as input for variant detection tools and for resolving ambiguity between variant callers (Koboldt et al., 2013a; Kothen-Hill et al., 2018). In addition, it has found broad applicability in diverse fields including tumor evolution, single-cell genomics, climate change ecology, and tracking community spread of SARS-CoV-2 (Miller et al., 2018; Müller et al., 2018; Paiva et al., 2020; Sun et al., 2020).