Supporting data for "Ximmer: A System for Improving Accuracy and Consistency of CNV Calling from Exome Data"
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Sadedin SP; Ellis JA; Masters SL; Oshlack A (2018): Supporting data for "Ximmer: A System for Improving Accuracy and Consistency of CNV Calling from Exome Data" GigaScience Database. http://dx.doi.org/10.5524/100495

Summary:
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While exome and targeted next generation DNA sequencing are primarily used for detecting single nucleotide changes and small indels, detection of copy number variants (CNVs) can provide highly valuable additional information from the data. Although there are dozens of exome CNV detection methods available, these are often difficult to use and accuracy varies unpredictably between and within data sets. 
We present Ximmer, a tool which supports an end to end process for evaluating, tuning and running analysis methods for detection of CNVs in germline samples. Ximmer includes a simulation framework, implementations of several commonly used CNV detection methods, and a visualisation and curation tool which together enable interactive exploration and quality control of CNV results. Using Ximmer, we comprehensively evaluate CNV detection on four data sets using five different detection methods. We show that application of Ximmer can improve accuracy and aid in quality control of CNV detection results. In addition, Ximmer can be used to run analyses and explore CNV results in exome data.
Ximmer offers a comprehensive tool and method for applying and improving accuracy of CNV detection methods for exome data.

Files:
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ximmer-master.zip - Archival copy of the github repository https://github.com/ssadedin/ximmer downloaded 14 Aug 2018. Ximmer is a tool designed to help users of exome and targeted genomic sequencing data accurately detect and interpret copy number variants. Please visit the GitHub repository for the most recent version. license: Lesser General Public License
ximmer-report-phs001272.txt - Ximmer report for the TruSeq samples analysed in the manuscript  are not available to the public due to  ethical restrictions on the dataset used. Readers are encouraged to contact the authors directly f they wish to gain access to these data.
ximmer-report-SRP010920.zip - Ximmer report for the Nimblegen samples analysed in the manuscript.
ximmer-report-SRP132744.zip - Ximmer report for the SureSelect samples analysed in the manuscript.
ximmer-report-SRP148622.txt - The Ximmer report for the Nextera samples analysed in the manuscript are not available to the public due to  ethical restrictions on the dataset used. Readers are encouraged to contact the authors directly if they wish to gain access to these data.

License:
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Lesser General Public License