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The detection of somatic point mutations is a key component of cancer genomic research, which has been rapidly developing since next-generation sequencing (NGS) technology revealed its potential for describing genetic alterations in cancer. We present MuSE, a novel approach to mutation calling based on the F81 Markov substitution model for molecular evolution
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, which models the evolution of the reference allele to the allelic composition of the matched tumor and normal tissue at each genomic locus. To improve overall accuracy, we further adopt a sample-specific error model to identify cutoffs, reflecting the variation in tumor heterogeneity among samples.
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After downloading the source file, for Unix-like operating systems please type the following commands sequentially in the command line to generate the executable:
For Windows, please install Cygwin (
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MuSE is comprised of two steps, which requires
The first step, ‘MuSE call’, takes as input (1) and (2). The BAM files require aligning all the sequence reads against the reference genome using the Burrows-Wheeler alignment tool (BWA), with either the backtrack or the maximal exact matches (MEM) algorithm  . In addition, the BAM files need to be processed by following the Genome Analysis Toolkit (GATK) Best Practices [3-5] that include marking duplicates, realigning the paired tumor-normal BAMs jointly and recalibrating base quality scores.
To speed up ‘MuSE call’, we recommend splitting the WGS data into small blocks (<50Mb) by using the provided option either ‘-r’ or ‘-l’, and concatenating all the output files by the Linux command CAT.
The second step, ‘MuSE sump’, takes as input the output file from ‘MuSE call’ and (3). We provide two options for building the sample-specific error model. One is applicable to WES data (option ‘-E’), and the other to WGS data (option ‘-G’).
The following commands briefly illustrate how to use MuSE. As to the preparation of BAM files, please refer to the first part, PRE-PROCESSING, of the Genome Analysis Toolkit (GATK) Best Practices ( http://www.broadinstitute.org/gatk/guide/best-practices ).
: Once you are ready to expose your uploaded files, you can publish them and make them visible and available to all Bintray users. Files can be published via the Bintray UI, or via the REST API, both as part of the
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. In some cases, uploading the files publishes them automatically, so you can skip this step.
You can resolve artifacts from and deploy them to Bintray directly using the Maven client.
You can configure your Maven settings.xml file to resolve artifacts through Bintray. The example below shows a settings file that is generated by Bintray.
To deploy artifacts using the Maven client, you first need to declare your Bintray credentials in the settings.xml file using your API key as your password (not your Bintray login password).
Then, add the the following Distribution Management section to your project’s pom.xml file to tell Maven to deploy into this package using the credentials you configured in the previous step.
You can resolve artifacts from and deploy them to Bintray directly using Gradle.
To resolve Maven artifacts from your Maven repository in Bintray use the following snippet in your Gradle configuration:
To deploy artifacts using Gradle you need to use the Gradle Bintray Plugin. For detailed instructions, please refer to the
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You can download a file directly using the following command:
To upload a file directly use the following command:
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is a one-stop-shop for Maven artifacts in Bintray. It is a large, popular, Maven repository that is managed by Bintray and is publicly available to all Bintray users.
As a Bintray user, you are able to include your public Maven packages in JCenter. As one of the most popular repositories in Bintray, this will expose your packages to many users and make them easier to find. Nevertheless, you retain ownership over your packages and are the only one who may update or modify them, and any changes you make are automatically updated in JCenter. Note that you cannot include any private packages (i.e., those hosted in a private repository) in JCenter because since all packages in JCenter must remain publicly available.
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offering some unique features to optimize development with Maven. You can configure a remote repository in JFrog Artifactory to proxy any public Maven repository on Bintray as follows:
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