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 caller...

Descripción completa

Detalles Bibliográficos
Autores principales: Khanna, Ajay, Larson, David E., Srivatsan, Sridhar Nonavinkere, Mosior, Matthew, Abbott, Travis E., Kiwala, Susanna, Ley, Timothy J., Duncavage, Eric J., Walter, Matthew J., Walker, Jason R., Griffith, Obi L., Griffith, Malachi, Miller, Christopher A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cornell University 2021
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8328062/
https://www.ncbi.nlm.nih.gov/pubmed/34341766
_version_ 1783732227544186880
author Khanna, Ajay
Larson, David E.
Srivatsan, Sridhar Nonavinkere
Mosior, Matthew
Abbott, Travis E.
Kiwala, Susanna
Ley, Timothy J.
Duncavage, Eric J.
Walter, Matthew J.
Walker, Jason R.
Griffith, Obi L.
Griffith, Malachi
Miller, Christopher A.
author_facet Khanna, Ajay
Larson, David E.
Srivatsan, Sridhar Nonavinkere
Mosior, Matthew
Abbott, Travis E.
Kiwala, Susanna
Ley, Timothy J.
Duncavage, Eric J.
Walter, Matthew J.
Walker, Jason R.
Griffith, Obi L.
Griffith, Malachi
Miller, Christopher A.
author_sort Khanna, Ajay
collection PubMed
description 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(1,2). 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.(3–6).
format Online
Article
Text
id pubmed-8328062
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Cornell University
record_format MEDLINE/PubMed
spelling pubmed-83280622021-08-03 Bam-readcount - rapid generation of basepair-resolution sequence metrics Khanna, Ajay Larson, David E. Srivatsan, Sridhar Nonavinkere Mosior, Matthew Abbott, Travis E. Kiwala, Susanna Ley, Timothy J. Duncavage, Eric J. Walter, Matthew J. Walker, Jason R. Griffith, Obi L. Griffith, Malachi Miller, Christopher A. ArXiv Article 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(1,2). 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.(3–6). Cornell University 2021-07-27 /pmc/articles/PMC8328062/ /pubmed/34341766 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Khanna, Ajay
Larson, David E.
Srivatsan, Sridhar Nonavinkere
Mosior, Matthew
Abbott, Travis E.
Kiwala, Susanna
Ley, Timothy J.
Duncavage, Eric J.
Walter, Matthew J.
Walker, Jason R.
Griffith, Obi L.
Griffith, Malachi
Miller, Christopher A.
Bam-readcount - rapid generation of basepair-resolution sequence metrics
title Bam-readcount - rapid generation of basepair-resolution sequence metrics
title_full Bam-readcount - rapid generation of basepair-resolution sequence metrics
title_fullStr Bam-readcount - rapid generation of basepair-resolution sequence metrics
title_full_unstemmed Bam-readcount - rapid generation of basepair-resolution sequence metrics
title_short Bam-readcount - rapid generation of basepair-resolution sequence metrics
title_sort bam-readcount - rapid generation of basepair-resolution sequence metrics
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8328062/
https://www.ncbi.nlm.nih.gov/pubmed/34341766
work_keys_str_mv AT khannaajay bamreadcountrapidgenerationofbasepairresolutionsequencemetrics
AT larsondavide bamreadcountrapidgenerationofbasepairresolutionsequencemetrics
AT srivatsansridharnonavinkere bamreadcountrapidgenerationofbasepairresolutionsequencemetrics
AT mosiormatthew bamreadcountrapidgenerationofbasepairresolutionsequencemetrics
AT abbotttravise bamreadcountrapidgenerationofbasepairresolutionsequencemetrics
AT kiwalasusanna bamreadcountrapidgenerationofbasepairresolutionsequencemetrics
AT leytimothyj bamreadcountrapidgenerationofbasepairresolutionsequencemetrics
AT duncavageericj bamreadcountrapidgenerationofbasepairresolutionsequencemetrics
AT waltermatthewj bamreadcountrapidgenerationofbasepairresolutionsequencemetrics
AT walkerjasonr bamreadcountrapidgenerationofbasepairresolutionsequencemetrics
AT griffithobil bamreadcountrapidgenerationofbasepairresolutionsequencemetrics
AT griffithmalachi bamreadcountrapidgenerationofbasepairresolutionsequencemetrics
AT millerchristophera bamreadcountrapidgenerationofbasepairresolutionsequencemetrics

Ejemplares similares