Cargando…

MuCor: mutation aggregation and correlation

Motivation: There are many tools for variant calling and effect prediction, but little to tie together large sample groups. Aggregating, sorting and summarizing variants and effects across a cohort is often done with ad hoc scripts that must be re-written for every new project. In response, we have...

Descripción completa

Detalles Bibliográficos
Autores principales: Kroll, Karl W., Eisfeld, Ann-Katherin, Lozanski, Gerard, Bloomfield, Clara D., Byrd, John C., Blachly, James S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866525/
https://www.ncbi.nlm.nih.gov/pubmed/26803155
http://dx.doi.org/10.1093/bioinformatics/btw028
_version_ 1782431927678009344
author Kroll, Karl W.
Eisfeld, Ann-Katherin
Lozanski, Gerard
Bloomfield, Clara D.
Byrd, John C.
Blachly, James S.
author_facet Kroll, Karl W.
Eisfeld, Ann-Katherin
Lozanski, Gerard
Bloomfield, Clara D.
Byrd, John C.
Blachly, James S.
author_sort Kroll, Karl W.
collection PubMed
description Motivation: There are many tools for variant calling and effect prediction, but little to tie together large sample groups. Aggregating, sorting and summarizing variants and effects across a cohort is often done with ad hoc scripts that must be re-written for every new project. In response, we have written MuCor, a tool to gather variants from a variety of input formats (including multiple files per sample), perform database lookups and frequency calculations, and write many types of reports. In addition to use in large studies with numerous samples, MuCor can also be employed to directly compare variant calls from the same sample across two or more platforms, parameters or pipelines. A companion utility, DepthGauge, measures coverage at regions of interest to increase confidence in calls. Availability and implementation: Source code is freely available at https://github.com/blachlylab/mucor and a Docker image is available at https://hub.docker.com/r/blachlylab/mucor/ Contact: james.blachly@osumc.edu Supplementary data: Supplementary data are available at Bioinformatics online.
format Online
Article
Text
id pubmed-4866525
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-48665252016-05-16 MuCor: mutation aggregation and correlation Kroll, Karl W. Eisfeld, Ann-Katherin Lozanski, Gerard Bloomfield, Clara D. Byrd, John C. Blachly, James S. Bioinformatics Applications Notes Motivation: There are many tools for variant calling and effect prediction, but little to tie together large sample groups. Aggregating, sorting and summarizing variants and effects across a cohort is often done with ad hoc scripts that must be re-written for every new project. In response, we have written MuCor, a tool to gather variants from a variety of input formats (including multiple files per sample), perform database lookups and frequency calculations, and write many types of reports. In addition to use in large studies with numerous samples, MuCor can also be employed to directly compare variant calls from the same sample across two or more platforms, parameters or pipelines. A companion utility, DepthGauge, measures coverage at regions of interest to increase confidence in calls. Availability and implementation: Source code is freely available at https://github.com/blachlylab/mucor and a Docker image is available at https://hub.docker.com/r/blachlylab/mucor/ Contact: james.blachly@osumc.edu Supplementary data: Supplementary data are available at Bioinformatics online. Oxford University Press 2016-05-15 2016-02-23 /pmc/articles/PMC4866525/ /pubmed/26803155 http://dx.doi.org/10.1093/bioinformatics/btw028 Text en © The Author 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Kroll, Karl W.
Eisfeld, Ann-Katherin
Lozanski, Gerard
Bloomfield, Clara D.
Byrd, John C.
Blachly, James S.
MuCor: mutation aggregation and correlation
title MuCor: mutation aggregation and correlation
title_full MuCor: mutation aggregation and correlation
title_fullStr MuCor: mutation aggregation and correlation
title_full_unstemmed MuCor: mutation aggregation and correlation
title_short MuCor: mutation aggregation and correlation
title_sort mucor: mutation aggregation and correlation
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866525/
https://www.ncbi.nlm.nih.gov/pubmed/26803155
http://dx.doi.org/10.1093/bioinformatics/btw028
work_keys_str_mv AT krollkarlw mucormutationaggregationandcorrelation
AT eisfeldannkatherin mucormutationaggregationandcorrelation
AT lozanskigerard mucormutationaggregationandcorrelation
AT bloomfieldclarad mucormutationaggregationandcorrelation
AT byrdjohnc mucormutationaggregationandcorrelation
AT blachlyjamess mucormutationaggregationandcorrelation