Bam-readcount -- rapid generation of basepair-resolution sequence metrics
Genomics
2021-07-28 v1
Abstract
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 . 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. Here we report on the release of version 1.0 of this tool, which adds CRAM support, among other improvements. It is released under a permissive MIT license and available at https://github.com/genome/bam-readcount.
Cite
@article{arxiv.2107.12817,
title = {Bam-readcount -- rapid generation of basepair-resolution sequence metrics},
author = {Ajay Khanna and David E. Larson and Sridhar Nonavinkere Srivatsan and Matthew Mosior and Travis E. Abbott and Susanna Kiwala and Timothy J. Ley and Eric J. Duncavage and Matthew J. Walter and Jason R. Walker and Obi L. Griffith and Malachi Griffith and Christopher A. Miller},
journal= {arXiv preprint arXiv:2107.12817},
year = {2021}
}