Dataset Information
MuCor: mutation aggregation and correlation.
Ontology highlight
ABSTRACT: 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.eduSupplementary data: Supplementary data are available at Bioinformatics online.
SUBMITTER: Kroll KW
PROVIDER: S-EPMC4866525 | biostudies-literature | 2016 May
REPOSITORIES: biostudies-literature
Publications
MuCor: mutation aggregation and correlation.
Bioinformatics (Oxford, England) 20160123 10
<h4>Motivation</h4>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 repo ...[more]